I like the windowed modes on some games, especially the Spiderweb games. They allow me to work on a project while the game is running in the background, and every so often I'll play through a bit more as a break. I think that explains why I'm just now getting through to Geneforge's ending, slower than the Avernum series. I always liked Vogel's work for the ability to play while doing other things and in not having to use a fullscreen mode.
In today's environ, I would seriously be on the lookout for more windowed or window capable games becoming feasable to play in such a manner, as they are getting quite popular. I believe the browser-based games and Flash games might have kept this alive and gave it a boost from the Windows 3.1 period of the windowed games boom.
As for multiple game instances, those are fun to play around with, like Fallout.