So far I really hated only the first Heretic II's boss, the Celestial Watcher, because he was way too strong, in a cramped space with no cover, so the only, to call it so, "strategy" possible was a frantic button pushing, a thing i really hate. It was the first and only time I had to cheat to beat a boss. Obviously I don't like wimpy bosses too, for example Quake II's final boss was way too easy.
For example I liked a lot Walton Simons in Deus Ex, that is very tough and normally you must face more than once to kill, almost doubling the fun.