I'm running into a real estate problem too, so you're not alone. With the X-Men, I actually feel pretty strong about displaying them with the bases. Especially since Gambit, Magneto, Colossus and Sabertooth all come with the various sections of a smashed Sentinel.
As for the rest, I decide on a case by case basis to display with or without the base. The Human Torch is one I definitely would not want to display without the base. He's a lot more "in-character" with his base rather than without it. Doctor Doom is another I prefer to display with the base, but moreso because I like that base a lot more than some of the others. The same goes for Thor. A lot of the other bases are non-descript enough that I don't really mind displaying them without their bases.