Any corrections are welcome to be discussed in the comments bellow.
color code:
Green - LAST boss of the instance is killable and rest of the instance does not have any major issues.
Yellow - Last boss can NOT be killed, atleast part of this instance is doable. Notes about these instances are in the comment bellow.
Red - None of the bosses are killable OR instance can not be entered.
Classic Dungeons
Ragefire Chasm
Deadmines
Wailing Caverns - last boss can not be killed
Shadowfang Keep
Blackfathom Deeps
Stormwind Stockade
Gnomeregan
Scarlet Monastery
Razorfen Kraul
Maraudon
Uldaman
Dire Maul
Razorfen Downs
Scholomance
Stratholme
Zul'Farrak
Blackrock Depths
Sunken Temple
Blackrock Spire
Classic Raids
Molten Core
Blackwing Lair
Ruins of Ahn'Qiraj
Temple of Ahn'Qiraj
The Burning Crusade dungeons
Hellfire Ramparts
The Blood Furnace
The Slave Pens
Underbog
Mana-Tombs
Auchenai Crypts
The Escape from Durnholde
Sethekk Halls
The Steamvault
Shadow Labyrinth
The Shattered Halls
The Mechanar
The Botanica
Opening of the Dark Portal
The Arcatraz - last boss can not be killed.
Magister's Terrace
The Burning Crusade raids
Karazhan
Gruul's Lair
Magtheridon's Lair
Serpentshrine Cavern - notes in the comment bellow
Battle for Mount Hyjal
Tempest Keep - notes in the comment bellow
The Black Temple
Sunwell Plateau
Wrath of the Lich King dungeons
Utgarde Keep
The Nexus
Ahn'Kahet: The Old Kingdom - only first boss can be killed, as you can't attack Taldaram.
Azjol-Nerub
Drak'Tharon Keep - Novos does not work, but instance can be finished.
The Violet Hold
Gundrak - Eck does not work, but instance can be finished.
Halls of Stone - achievement from tribunal will not be gained, but loot and fight works well.
Halls of Lightning
The Oculus - first boss works well, others don't.
The Culling of Stratholme
Utgarde Pinnacle
Trial of the Champion
Forge of Souls
The Pit of Saron
The Halls of Reflection
Wrath of the Lich King raids
Obsidian Sanctum
Naxxramas
The Eye of Eternity
Vault of Archavon
Ulduar - first 4 bosses work.
Trial of the Crusader
Onyxia's Lair
Icecrown Citadel - first 2 bosses work.
Ruby Sanctum
Cataclysm dungeons
Blackrock Caverns
Throne of the Tides
The Stonecore - notes in the comment bellow
The Vortex Pinnacle
Grim Batol
Halls of Origination
Lost City of the Tol'Vir
Deadmines
Shadowfang Keep
Zul'Aman - notes in the comment bellow
Zul'Gurub - last boss can not be killed.
End Time
Well of Eternity
Hour of Twilight
Cataclysm raids
Blackwing Descent - last boss of normal mode can not be killed, therefore heroic mode can not be accessed.
The Bastion of Twilight
Throne of the Four Winds - notes in the comment bellow.
Firelands
Baradin Hold
Dragon Soul