I'm not sure if he really counts as boss here... but the boss I remember the most was Kanrethad ebonlocke. This fucker... so many tries... so many evenings. And then, as he finally fell. Best feeling I had from this game in a long time.
Iskar will go down as one of the more memorable fights for me. The Eye mechanic was really unique. Iskar and the Arrakoa were by far the best part of WoD, and Iskar's voice lines are really well done.
Thaddius was extremely fun when it was current, the kind of fight that didn't feel too gimmicky. During Vanilla, the charge mechanic was really unique for its time.
Cho'Gall was really damn intense at the time and has one of my favourite enrage phases.
Lei Shen is hands down one of the flashiest and fun fights ever.
Mythic Imperator Mar'gok, without question. Not because of the fight quality or anything within the game, but everything about the context of the kill (poor performance, last last last pull before the guild left for holiday break)...I've never felt so emotionally drained. You can hear the stress drain out of everyone at the kill. I can't post links, but it's "Duality vs Mythic Imperator Mar'gok" if you want a good laugh.