Yeah, windowed mode does seem to help quite a bit, but lo and behold my video card likes to have a freak out party after like 10 mins in windowed mode with skyrim. Screen turns to fuzzy lines then freezes forcing hard reset. Do you need the skse with the simple border-less window mod? And, would it make a difference if I already have problems in regular windowed mode?
What video card and drivers are you using? That's very weird that it would do that in windowed mode but not in full-screen mode. I would say that it sounds like an overheating problems, but if you don't get that at all in full-screen mode, then something else is wrong.
The borderless window mod doesn't require SKSE, but it's compatible. Also, there's another mod that someone mentioned that's really an AutoHotKey script that does the same thing, so you don't have to use an exe file. However, these mods merely move/resize the screen so that it appears like you're running full-screen. They use the windowed mode, so if you have trouble with it normally, they won't help. However, I would try to track down why you're having problems running it, because it could expose other problems with your system. Could it be crossfire or anything like that?
You won't be able to use crossfire with windowed mode, and the in-game gamma settings don't seem to work. I have spent a lot of calibrating my TV and monitors, so the default setting is perfect for me (and how I think it's "meant" to be played). You should be able to use the graphic driver to change those settings anyway, although that would obviously change things globally.