Well, I'll give my opinions for the categories that won't cause flaming.
Best instance: I've always loved Black Castle, maybe because it was the first group dungeon you can do, but I just really enjoyed it, especially the Raiders of the Lost Ark ball. Another favorite would be Sanctum of Burning Souls.
Worst instance: Probably Prison Colony in Thunder River. The loot there was absolutely crap and it visually did nothing for me. Probably my second least favorite would be Cradle of Decay.
Best raid: Overall, I'm gonna go with T3 before they nerfed it so much. Best boss fights in the game will probably be Thoth Amon and Yah Chieng.
Worst raid: Guess I really can't pick as they are all good, but I will highlight raid bosses I can't stand: T2 Incubus/Succubus (stupid fears and kb's ugh), T3 (absolutely hate the new Louhi, why'd you change it Funcom?), T4 Imp (ffs, reduce his hp already!)
Best music: My favorite is the music in the Stygian zones, but all the music is good, none that I don't like.