Well, first and foremost, you can find an expendable Minimate to use as a "holding dummy." Meaning: say you want to paint just a hand, and it's too difficult to just take it off and set it on your desk (it rolls around too much). You can take the hand and insert it into the correct socket in your disposable Minimate, and paint away--without worrying about damaging the "holding dummy."
Second, use tape. If you're using spray-paint, or an airbrush, masking and modelling tape is an invaluable tool. You use it to tape off any part near to your current work space that you don't want painted. It's also good for making clean, straight lines with brushes. This is the kind I use: Tamiya Masking Tape. It's really good stuff, and comes in tons of sizes. The smallest, I think, is 6 mm wide. And, it's pretty cheap--3 bucks for a "refill" roll, or about 5 for the roll with the really good dispenser. If you have problems with the paint bleeding through underneath the tape, IT'S NOT THE TAPE. IT'S YOU. You have to get it very tight, have it on all the way.
Hope that helps.