The two types fulfill different functions; therefore, in an ideal campaign, I would mix the two (obviously, there would be more small dungeons - there is no need for more than one or probably two really big ones). Small dungeons can be "completed", and I think many players like that feeling. They are also easier to build around a theme. But larger dungeons - at least 50 rooms - open up strategic possibilities and complexity you simply can't cram into a small structure. For example, inter-level exploration obviously needs multiple levels. You don't get that incredible feel of exploration and being lost in an immense thing if it only takes a few sessions to clear it out. Big dungeons can't, and shouldn't ever be cleared!
In practice, I don't have the time or patience to design a proper megadungeon, so I only make small and occasionally medium ones... my "dungeon" is the wilderness.