Not my list, but I found on a hunter site. Great info to have if you think that tranq shot became totally useless with BC.
Azshara: Maws [Quest NPC]
Burning Steppes: Klinfran the Crazed [Hunter Epic Quest NPC]
Winterspring: Artorius the Doombringer [Hunter Epic Quest NPC]
Molten Core: Magmadar [Boss]
Blackwing Lair: Death Talon Seether [Trash], Chromaggus [Boss] & Flamegor [Boss]
Zul'Gurub: High Priest Thekal [Boss] & Hakkar the Soulflayer [Boss - but only if High Priest Thekal remains up]
Temple of Ahn'Qiraj: Qiraji Slayer [Trash] & Princess Huhuran [Boss]
Naxxramas: Gluth [Boss]
Terokkar Forest: Slaag [Quest NPC]
Black Morass: Aeonus [Boss]
Shadow Labyrinth: Cabal Zealot (in Demon Hound mode) [Trash]
The Arcatraz: Soul Devourer [Trash]
Underbog: Lykul Stinger [Trash]
Serpentshrine Cavern: Tidewalker Warrior [Trash] & Underbog Colossus [Trash]
Hyjal Summit: Ghoul [Trash]
Black Temple: Leviathan [Trash], Ashtongue Feral Spirit [Trash], Bonechewer Brawler [Trash] & Hand of Gorefiend [Trash]
Zul'aman(Upcoming Instance): Amani Bear [Trash], Amani Bear Mount [Trash], Amani Dragonhawk [Trash] & Halazzi [Boss]
While not a common strategy, Tranquilizing Shot can also be used on Hunter pets when they gain 'Frenzy' from the talent in the Beast Mastery tree, in PvP situations. Note: This is not the same as Beastial Wrath, which cannot be removed in this manner.