I'm considering Upgrading to Windows 7, and i am wondering if someone can tell me how compatable the GECK is with it. Are there any major conflicts i should be aware of, or modding issues, or anything like that?

Dont install the game in the default location. Install it on your C root drive, or another drive altogether.

The Program Files folder is protected and does not work well with the GECK.

I had vista-32, and upgraded to 7-64 bit and it works just fine. I have no issues with it. I had some with vista, but none on 7. As to what WillieSea said, all those issues go away, as long as you ALWAYS run everything that has to do with modding as administrator. This includes the Fallout Launcher, GECK, FOMM, and Fallout 3. As long as you run these things as administrator whenever you use them, and are using an administrative acount (which on a home PC you should be on one) none of the normal issues occur. This is because your program files are protected by UAC (User acount control) but not other places like your C drive. If you dont run things as admin, it blocks them from opening files, or saving. So if you want, or need, to install it to the default place, simply run everything as administrator.