I guess I should have clarified from the beginning that I'm a Mac user, waiting for the Mac version of Aquaria. I tried the demo in Boot Camp, but didn't play very far for fear of getting hooked and just buying the Windows version (besides the plus of not having to boot into Windows, I want to support Mac native game development wherever it happens).
Here's a fine specimen of an options dialog, captured in far-away Maclandia:

(you've probably already seen it; don't you have a summer house in Maclandia or something?) The resolutions that don't have (stretched) next to them appear in centered 4:3 mode. BUT...many games on the Mac have a predefined subset of resolutions they allow, and they often don't include the non-stretched versions.
Ideally, all games that don't support rendering to anything but 4:3 would include the ability to pillarbox the output. Ahh, dreams of an ideal world...
I've only just started to get into Windows gaming, so I don't really know what the situation there is like. Are you telling me that I can set an option in my video card driver utility and all games will respect it? Interesting...