The only raid boss encounter that sticks out in my mind for all of these years, and the reason may shock you, is Hellfire Assault and for the reason of all of the fucking downtime that happens. Even back when it was current content the amount of time of not doing anything was unbearable.
Probably an overly critical take on such a minor aspect of the fight that does not technically have to do with the mechanics of the boss, but in my opinion, substantial enough.
For dungeon bosses I feel that Shirrak the Dead Watcher in Auchenai Crypts (TBC) has the absolute worst design for a boss. 200% increased casting time to spells/abilities? Just RIP any caster/healer that comes in. I understand that you have to move around in order to deal with this but take the scenario of a bunch of random people who have either A.) never been here before (TBC Classic is gonna be fun), B.) been so long and have forgotten, or C.) not paying attention (almost always an issue)... fuck that boss.