I've played Fallout 3 extensively on X360, that was the first platform I played it on. I loved it on there lack of mods aside, it was great. I just recently picked up the GOTY on PC and I've been putting time in a bit of time on that..
So far, I find the visuals on console are better. Everything looks grittier on console compared to PC. PC has great lighting, superb draw distance but the textures just look to smooth and don't look as dirty. In this case, grittier is better I find it matches the atmosphere and environment of Fallout. Settings are on ultra high, so all visuals are at their maximum. PC does have a much smoother frame rate.
But the mechanics on PC were better overall, shooting, moving it all flows seamlessly on PC. Except I found lockpicking to be a little harder, the controller on 360 is better at making fine adjustments when looking for the "sweet spot". Using terminals was a little confusing at first. Unlike lockpicking it didn't show how to exit. I was hitting the E button for quite awhile thinking it would take me back just like it did when I picked a lock. But after re-loading 2 times, I found out you have to move the mouse pointer on the power button on the terminal screen itself. The lack of instruction is my only gripe there.
I also found the character models looked smaller on PC. But that might be because my TV is 40" vs. my monitor which is 20".
Oh and, I've yet to install the DLC. It takes forever for it to even read the disc. I heard that's normal, but when I did finish installing Windows said it didn't install correctly.