The GOG version has the newest official patch, I believe.
The version from Bethesda's website includes the patch, but it is not automatically installed. (Installing it is *highly* recommended; this game has a reputation for being buggy, and the unpatched game is even more buggy than the final version.)
There are some other little mods floating around, like one apparently from CompUSA; some fan installer might install some of them. I have not tried them myself.
Whichever version you choose, remember to save early, often, and in multiple slots; this game earned the nickname Buggerfall (and the developer the name Bugthesda) for a reason. Unfortunately, the game only has 6 save slots; if you need more, you will need to back up your saves.