Ours is one big collection, mostly because I can't trust Ronalopolis to even come back and say hi to all of you, let alone keep tabs on what we have. I use VG Collect mostly for making sure I'm not buying a double of something when I'm out at the thrift shops and flea markets, and checking two databases would be even more unwieldy than the one we have now.
It's funny though. We are both video gamers but the games we play are so different that it's almost like two different hobbies. We rarely game together. Instead, a lot of nights are spent with him playing the latest shooter on the TV and me pausing some RPG on the DS when his cutscenes come up, watching them almost like a movie in between my game. So if we ever had to divide our collection for any reason, there would be very few arguments about which games went with who. Those games we can play together seem to be among our favorites though, because we can enjoy them together.