For me personally i would say the 3 hardest encounter i've come across was:
1. M'uru, Oh my god after the first 3 days of whipes i still saw no sign of improvment it was for good reason called "The guildslayer", so much frustration and anger over that fight feelt impossible although after a week or so we started to make some improvment but my god it was nothing i had encountered before! The feeling when he finally went down is one of my brightest memories i have from this game. I very much doubt i ever will come close to that feeling again. There was no different difficulties bullshit we have today either your good enough (atleast improve over time) to kill the boss or you're not simple as that.
2. LK heroic for me probably the most "epic" fight so to speak being the the Lich king and all took a good month from reaching him until downing him but oh man the feelings when i look back at it, you just dont get that today, unfortunately.
3. Kae'l Thas i know i expected him to be hard but as you could fairly easy roll over the first Fel reaver and that other geomancer guy i didnt expect him to be that fucking stronk, The bird took some time to down but Kael'Thas probably one of the most diverse raid encounters to the day, flyin weapons legendary shields and shit that was sick.