EDIT: Scratch what I said about the low framerate - it was a problem on my end (once in awhile, games will dip to unplayable framerates and I just need to reboot, still not sure what that's about, I went to play LIMBO and still got 12FPS so I knew that was the case). After downgrading to 1.4 using the patch I can't link, it's actually working perfectly in Surround. So long story short, just find the 1.4 patch, install to a temporary location, replace the files in the Steam folder, and apply fixes as normal. Select 16:9 aspect ratio in the game's settings. Perfect 60FPS with all settings jacked up. I'd try with Doom 3, but I'm waiting for the BFG edition to play that again.
I realize it's been awhile since you made this comment, but it seems you're still active here so I'll reply with my recent (tonight) experience.
I was able to get Prey to work in Surround, but with a caveat: the framerate is completely unplayable, and it involved "downgrading" to pre-Steam patch. The Steam forum suggests that enabling "single monitor performance mode" in the nVidia drivers is the fix for the bad framerate, but that's an impossibility for playing in Surround. Perhaps this will work for you though if you have a Crossfire setup.
I downloaded the Prey 1.4 "patch" from here:
Actually I can't provide the URL because it's apparently triggered the spam filter. I Google'd for "prey 1.4 exe", it's the first result, titled "Prey v1.4 Patch Download, Prey Patches".
While I can't open the executable as I normally would with 7-zip, the installer apparently does not care if Prey is even actually installed. Install it to a temporary directory, and replace the Steam files with all of the files the patch installer extracts (Windows 7 just paste directly into the folder and Windows will merge and replace as necessary). From there, follow the multi-monitor instructions from the
WSGF report. The exception is that the aspect ratio should probably be 16:10 (or at least it was for me).
Either way, the game itself (at least the modern one) works fine in multi-monitor at 16:10 with the exception of the framerate thing. That happens for me on both the 1.4 and the post-steam-patch versions. In triple-screen, though everything worked aside from the menus being stretched, I was unable to get more than about 8FPS. Without the multi-monitor, I'm getting a solid 30FPS, so I might try to play it again in single screen.
As a fun side note, looking at Google results for "tweaking" this game back in 2008 noted that your framerate should be at least 15FPS for a solid experience. Did we really tolerate that back then? Also there was a general lack of real knowledge back then about what most of the game settings actually do, for example what VSync was. Fun trip down memory lane.
Anyway I'll keep looking to see if I can find some sort of other fix for the framerate. It's odd because it happens even in the menus.