1. Spec and glyphs

Typical Sub PvE build suggested by various guides looks like that: 8/2/31
However, it is somewhat flexible, and can be modified to increase survivability by fair margin (Enveloping Shadows or Cheat Death talents), but it'd lead to some dps loss.

Talents taken go as follows:

Assassination
Coup de Grace 2/3 - to improve Eviscerate which is main finisher after all 3 timers, ie. SnD, Recuperate and Rupture are on safe duration. It's somewhat strong talent, because Evisc is very frequently used in spec, and also it's multiplicative with Subtlety mastery, Executioner. However, it's not as strong as Lethality and is mainly taken to reach tier 2 in Assassination tree.
Lethality 3/3 - is pretty much a must, due to very high crit chance of Backstab, which is main source of damage, with values close to 40%, changes it's crit modifier to x2.3.
Puncturing Wound 3/3 - mandatory as well, working in synergy with other talents, mostly Lethality, increasing Backstab crit chance by a very large margin (30% at rank 3)

Combat
Precision 2/3 - considering very low EP value of hit for Sub, it's somewhat lacklustre talent, much weaker than for Assa specs, used mostly to spend remaining talent points and negate some hit rating requirements, effectively increasing more beneficial ratings, typically haste.

Subtlety
Improved Ambush 3/3 - with relatively good gear it makes Ambush a certain crit, with addition to increased dmg. Taken to increase Shadow Dance power.
Relentless Strikes 3/3 - mandatory due to high energy requirements of both Ambush and Backstab (40 energy after talents for each), makes every finisher to restore 25 energy, assuming you use it with 5cp, which you will usually do
Elusiveness 2/2 - strong talent, increases both dps and survivability by reducing cd on both Vanish and Cloak of Shadows by a fair margin (1 min and 30 sec respectively)
Opportunity 3/3 - no-brainer, increases dmg of Ambush and Backstab by a very large margin.
Initiative 1/2 - pretty much a filler talent, makes Ambush add another combo point from time to time, which almost always leads to capping combo points during Shadow Dance. It often allows rogue to start with 5cp finisher after Vanish when paired with Preparation (without HaT proc), therefore it's somewhat dps increase.
Energetic Recovery 3/3 - a must, makes each Recuperate tick to recover 12 energy, which leads to much smoother rotation.
Find Weakness 2/2 - must-have, makes auto attacks, Eviscerate, Shadow Danced Ambushes and subsequent Backstabs much stronger for a limited amount of time, even more so with Sub passive skill, Master of Subtlety
Hemorrhage 1/1- even if not as strong as Backstab, hemo provides +30% bleed dmg debuff and 24 sec DoT if glyphed which should be ticking at all times if done so. It's also needed for Sanguinary Vein.
Honor Among Thieves 3/3 - at 3rd rank it gives certain combo point on current target if ANY person in raid/party crits with either damaging skill/spell or heal (tho healz don't crit rofl), it has 2s cd, but I can't really tell if it does on Warmane, some ppl claim it doesn't, which would make it exceptionally strong. Also applies raid-wide +5% crit buff if you lack feral druid or fury warr. Pretty much no-brainer, needed to operate properly as Sub in PvE environment.
Premeditation 1/1 - not required, but quite nice talent, which adds temporary 2cps to current target, if taken, it should be macro'd to Vanish, Shadow Dance and Ambush, to secure highest possible usage.
Preparation 1/1 - adds some utility by refreshing cd on Sprint and Shadowstep, Vanish cd reset is direct dps increase because of Find Weakness
Sanguinary Vein 2/2 - although not as strong as in newer patches (10% dmg increase on bleeding targets compared to 16% later on), it's still strong talent, w/o reliance on other ppl in group because of Hemorrhage-Rupture link
Slaughter from the Shadows 3/3 - another mandatory talent, makes Backstab spam way more manageable (reduction from 60 to 40 energy cost), also reduces cost of Ambush by the same amount, and gives mild reduction to Hemorrhage and Fan of Knives.
Serrated Blades 2/2 - makes Eviscerate to refresh Rupture duration with 100% chance at 5cp, a must
Shadow Dance 1/1 - as nearly any top talent, mandatory for spec, increases dps by quite a lot, by raising Find Weakness uptime, and giving opportunity for quite impressive Ambush spams

If you would like more survivability, it's best to take points from Initiative, Premeditation and Preparation and place them in Enveloping Shadows and/or Cheat Death with first being exceptionally strong in fights with abundance of AoE dmg taken. Apart from that, due to natural ~100% uptime on Recuperate, Imp. Recuperate instead of Precision might be somewhat viable.

Glyphs used are:

Prime
Glyph of Backstab - self explanatory, Backstab's high crit chance makes it very large energy gain
Glyph of Slice and Dice - since you can't refresh SnD in Sub with other finishers, that glyph is mandatory, it loosens rotation by quite a bit, effectively giving high dps gain
Glyph of Hemorrhage - not as strong as previous two, but still viable option, DoT left by hemo is affected by +bleed dmg debuff, also it's twice as strong if it's left by crit (DoT itself can crit as well).
If you don't feel like weaving hemo into rotation, glyphing Eviscerate or Shadow Dance can be viable, with first give some sustained dps increase and 2nd being more of burst choice.

Major
Glyph of Tricks of the Trade is usually 1st in line, giving free TotT for a small price of 33% effect loss. Another good choice is Glyph of Feint, which does the same for Feint, w/o any disadvantages. Last glyph is a matter of taste tbh, EJ states Sprint or FoK are the best in the spot, though it's arguable, some other glyphs provide situational bonuses worth looking at, like Glyph of Kick (mostly 5man glyph tho), or Glyph of Cloak of Shadows e.g. if you somehow manage to overaggro with that frequent Vanishes.

Minor glyphs provide close to 0 utility, therefore it's totally a matter of taste.

2. Rotation

As many other specs in game, Sub relies on priority system on both finishers and combo points builders, and it isn't particularly easy, with as much as 4 timers to watch , not including cds and items' icds.

For building combo points choice is
Ambush>Hemorrhage (if DoT not present and it's glyphed)>Backstab>Hemorrhage (when you can't stay behind the target)

Recommended finisher priority goes as follows:
Rupture>SnD>Recuperate>Eviscerate

Ideally you finish with Rupture only once, so it'll be the highest dmg per energy move by far, being constantly refreshed by Eviscerate. All finishers should be used @ 5cp, especially Eviscerate, failing might lead to messy cycle, which includes dropping Rupture from target - in that case you either Vanish and reapply it or just reapply w/o Master of Subtlety buff (with it's priority below SnD then). SnD due to gyph might be refreshed with lower amount of cp if needed w/o much loss, about 3-4 should be fine if you can manage.
Whatever you do, remember to don't clip SnD/Recuperate much, ideally you want them to be refreshed in the same time they wear off, but it might be unachievable due to chaotic fight and/or lag. More practical choice is to refresh with <3s left with exception of Rupture which should be refreshed as often as you get 5cp and can Eviscerate to avoid losing HaT proc. 3s buffer makes it fairly safe option and also avoids losing last tick of Recuperate. If you're close to it on either SnD/Recuperate with 5cp, wait a bit and pool energy in the mean time (ie. save it for finisher followed by either cp builder).

Sub has 4 main cooldowns:
Shadowstep - short and nice cd, which teleports rogue behind the target, it has 25yds range and 24s cd, therefore should be available when needed. If you have typical "Patchwerk" fight always keep it for extra Ambush dmg after Vanish/Shadow Dance, if it's movement fight, it might be wiser to keep it for returning into fight after movement and/or fast positioning for Backstab/Ambush. Another use is 3s increase in movement speed, so it might be certain alternative to Sprint.

Vanish - with 2min cd it's not as strong as Shadow Dance for dps, but still makes it's impact. Gives Master of Subtlety buff + Find Weakness from Ambush therefore it's best to use it on Eviscerate cps for extra burst or on special occasion when you drop Rupture. Also best used on 0cps if you have Premeditation, in that case Premed+Ambush will give you 5cp

Preparation - being 5min cd makes it a bit unappealing, you might keep it for some utility or just Prep after using Vanish for more Find Weakness uptime

Shadow Dance - the strongest Sub cooldown in the terms of dps gain, with only 1min lock, and whole 6s of stealth-only moves spam outside of stealth. Should be used on healthy levels of energy, you might even cap it for a moment, to assure biggest gain. Just like Vanish 0cp is best because of high combo point gains from Ambush, and also if you Shadowstep and Ambush, keep in mind that Ambush is affected by Find Weakness, so Shadowstep before 2nd one. Unlike Vanish (and simple Stealth ofc) it doesn't give Master of Subtlety.

Priority for cooldowns should go from shortest to longest so:
Shadow Dance>Vanish>Preparation
Shadowstep not included, as it's mileage varies on each fight, and it's pretty dynamic cd, as written above.

Weapons used should always be daggers, with mh as slow as possible (at least 1.8), and oh as fast as possible due to poison used. As for poisons themselves, Instant on mh, Deadly on oh, and Wound or Instant on thrown weapon if you will FoK. AoE power of Sub is underwhelming though, it has the weakest FoK of all 3 specs, and also doesn't have cleave abilities like Combat, so it might be better to just respec if you need strong AoE or just tunnel-vision 1 mob and do regular single target cycle.

There is possibility of using Combat-alike weapons, so regular slow 2.6+ mh and fast daggger in oh, but it's questionable, since you wouldn't be able to do Backstab in that case and Hemorrhage itself is kinda underwhelming (Backstab's dmg is 364%+1634 and Hemo 223%+additional 89.2% nonstacking DoT, 154%+61.6% if not using dagger), and it'd be better to just go Combat with such weapons.

Opening fight
It's best to keep 5cp on last trash target before boss, it gives the most comfortable situation for starting fight (5cp SnD prestealth). If you somehow cannot do it, don't worry, combo points are easily collected and you won't lose much.
Anyway, best scenario for opener would like like this:
  1. 5cp Slice and Dice
  2. Prepot (optional, use 1200 Agi potion)
  3. Stealth
  4. Tricks of the Trade
  5. Shadowstep
  6. Ambush
  7. As soon as you leave stealth 5cp Rupture (if you don't have enough cp, 1 Hemorrhage if glyphed, otherwise Backstab)
  8. Hemorrhage if wasn't used in previous step and you need DoT and/or debuff

After that it goes pretty smoothly, unless you have positioning problems due to fight mechanics. As soon as Find Weakness wears off, do 5cp finisher if needed and pop Shadow Dance.

3. Stat priority

Since main sources of damage in Sub are Backstabs (usually by far) combined with autoattacks and sometimes Ambushes, you should strive to get as good mh as possible, as it's dps' EP is just outstanding, being around twice as valuble as another main stat, Agility. Worth adding, some special ridiculously slow daggers might be better than higher lvl counterparts for sheer Backstab spam, though keeping it simple, higher dps = upgrade when dagger is 1.8+.

Agility is also extremely strong stat, increasing both AP and crit chance (also it adds some survivability from dodge, but nvm), it improves every damaging ability, scales with every offensive 2ndary stat, and on top of that, is multiplied by both BoK/MotW buffs and Sinister Calling, with 2nd being large 30% extra. Due to that, it's EP is reported to be ~3.6 with T11 gear lvls.

After that it can be pretty much anything, with +hit being very strong up to around 8% (I'm unsure about the cap on Warmane, might be as well ~9% like I had to go on WotLK with hunt, had special attack miss @ 8.65% hit here anyway) with EP ~1.4, then haste being the most beneficial and very close to hit's value before capped (around 1.4 EP as well).
Expertise should be capped, but since dummies can't parry/dodge on our server I can't really say how big is the dodge cap, naturally it should be 26, but just like on WotLK, values like 21-22 could be sufficient. Some feedback on that matter would be valuable. Anyway, after mentioned caps and haste stats values seem to flatten, with crit being the most beneficial, and mastery the least along with white +hit cap (spell hit cap is very low in value as well due to lack of poisons-oriented talents).
As a rule of thumb - you should reforge mastery and hit, if past yellow cap, into more valuable stats, ideally haste.

Simple stat order would look like this (regardless of gear, unless very specific):

WDPS>Agi>Hit (8% cap)>Haste>Expertise (dodge cap)>Crit>Hit (17% cap)>Mastery>Hit (27% cap)

Main reason for mastery being so low, is rather small impact on dps by both Rupture and Eviscerate. It improves SnD haste, but value for each % of haste is much higher than on regular haste.

As for gems used, Delicate Inferno Ruby should be used in almost every slot, except helm (if it doesn't have red socket ofc), and if socket bonus is at least 20 agility with only 1 socket not being red. Meta of choice only Agile Shadowspirit Diamond. If you go for socket bonus, use Agi+Haste gems in yellow sockets, and Agi+Hit in blue.

4. Proffs & Enchants

Enchants used:
Head - Arcanum of Ramkahen
Shoulders - Greater Inscription of Shattered Crystal
Cloak - Major Agility, slightly worse alternative is simple +50 crit rating enchant
Chest - Peerless Stats if you can afford it, otherwise cheap +15 to main stats is fine
Bracers - Agility, as above, if you can't afford, there's cheap alternative with +50 haste rating this time
Gloves - Major Agility is the best choice, might be replaced with +50 haste
Legs - Dragonscale Leg Armor
Shoes - Major Agility
Weapons - double Landslide is on top by a large margin, after that it can be double Mongoose, Berserking or just Hurricane
Don't forget to apply belt buckle as well, with another agility gem

Most valuable profession seems to be Engineering with Synapse Springs you can macro to Shadow Dance for some healthy burst. After that JC is the best with 81 agility bonus from JC-specific gems, which is a whooping 1 agi more (lol) than BS, Enchanting, Inscription, LW and Alchemy. If you don't use Flasks and/or Elixirs, Alchemy is 2nd best on Warmane because you can stack both cata and wotlk alch-specific flasks at once for bonus 120 agility. Tailoring is the weakest crafting proc in terms of dps gain, since ap isn't modified by Sinister Calling nor buffs. If you need gathering proffs, Skinning and Herbalism might be somewhat helpful in dpsing, nevertheless they are the worst choice for pure dps along Mining, which has no benefit, except bonus stamina.

Choosing race is imo subjective, but if you go for the Recount's top, on Ally dogs are the strongest with bonus 1% crit, on Horde Trolls with their Berserking. EJ states Nelf is the best Sub race overall, though I'm Fairly certain Shadowmeld isn't considered a proper stealth and you can't Ambush from it, but if you indeed can, that makes them the best w/o question since you would get both more Find Weakness uptime and also (possibly) tasty Master of Subtlety buff for a few seconds.

5. Other stuff

As I wrote somewhere above, if you go for build with Premed, make a macros with it for Shadow Dance, Ambush and Vanish. Simple ones would be like:
Code:
#showtooltip
/cast Premeditation
/cast Ambush
Code:
#showtooltip
/cast Shadow Dance
/cast Premeditation
/cast Ambush
Code:
#showtooltip
/cast Vanish
/cast Premeditation
/cast Ambush
Ambush in ShD and Vanish macros is to ensure it goes off asap, since both abilities are off-gcd. It's also a nice idea to add /startattack into Hemorrhage and Backstab, but some might argue as it might as well lock autoattack here and it hurts.
Other than than it's pretty standard, might as well do w/o special macros, though you'd like Tricks of the Trade macro if you gonna use it. EJ's suggested macro looks like that:
Code:
#showtooltip
/cast [@target,noharm,exists][@focus,exists,nodead,noharm][@targettarget,exists]Tricks of the Trade
To manage cooldowns and SnD/Recuperate/Rupture more efficiently you want some addon with configurable timers, it might be ForteXorcist or just Power Auras, and that's about it. Other addons are just a matter of taste.

TL;DR - Sub is awesome spec and it's a lot of fun to play, if you got rogue, just try it.

PS. Guide uses large portions of info provided by EJ forums, including their own Compendium, so you should thank them first if you would, I just rewrote it and added a bit. I didn't care about looks, so no 'qq y u have no pics n colors' pls.