Hmm, perhaps there could be another approach. Like lying to the certain applications about the resolution of the 'screen', to return the dimensions of the primary monitor, and then map coordinate 0,0 to the location we want the app to start at.
I'd have to get home and boot up Linux to try them out, but the ones coming to mind are Darwinia, Trine, and World of Goo. Is there a way that I, as a user, could manually set that fullscreen hint?
Setup has always been a very minor annoyance, but as a gamer who uses multiple monitors, Linux has been a simple no-go for me. I proselytize Linux everywhere, but is mostly just a development platform for me, because of this combination. I recently got on the Steam for Linux beta, and it's fantastic. But most games I have to play in windowed mode, and some I just can't play at all, because it spans across my two screens (with very different dimensions and resolutions). Sure, I could disable one monitor, but that's more trouble than it's worth, when I can still take advantage of my 2nd monitor just fine in Windows. In Windows, games only fullscreen on one screen, I can still see my gmail feed just fine on my second monitor.
Linux does a lot of things very well, but multiple monitors has always been a bit of a mess when fullscreened apps are involved.