I remember seeing someone saying on here a while back that you shouldn't have Fallout 3 installed in C:\Program Files\ if you're running Vista or 7 if you wanna mod or it messes things up. I got the GotY via Steam, and that's literally the only way it can be installed when you get it from them. Am I going to encounter severe issues or what?

You could always move the folder and then hack the registry path to point to the new location...I think that should work out fine, but I also have no experience with Steam.

Easiest solution is to install Steam itself to a custom directory.

Install Steam to "C:/Games/Steam" and all you Steam games will be installed to "C:/Games/Steam/Steamapps/" and you'll never have a problem with UAC or shadowing or permissions or any of the other stuff that can potentially be a problem.

Wow, I'm an idiot. No idea how I didn't think of that. Thanks.

Or if you just run the geck as administrator you dont run into any problems related to this issue... (And that only takes like 3 clicks)

It's not just the GECK that can cause a problem. Shadowing and UAC permissions can also cause problems with getting mods to run and with FOMM. You can work around it, and setting things up right avoids a lot of the issues, but it's just easier to install elsewhere.

Personally I run without UAC enabled, but that's not something I recommend for most users. I have Fallout 3, Morrowind, and Oblivion in c:\games\bethesda softworks but I spaced it when installing Steam, and that means it, and Fallout: New Vegas, are in the C:\Program Files (x86) folder.