The hardest regular must-face bosses are probably Materia Keeper, Lost Number (well, depending on at which stage of the game you face him) and Demon Wall. Well, they are about the only bosses in the game that I constantly see help threads for at GameFAQs' FF7 message board. They pop up like there's no tomorrow. And yes, those 3 can all be pretty challenging if you're underleveled and/or don't know what strategy to use.. probably more difficult than any other boss in the game, except Emmy and Ruby. At least they are the 3 bosses I remember having the most trouble with during my first playthrough at least (especially Demon Wall).
EDIT: Realized Lost Number isn't a must-face boss, and I'm not sure I even fought him on my first time through. But anyway
