Steam has the GOTY edition, and I know EB Games sells it. If you're in America, I assume any EB Games/GameStop stores would have a copy as well.
I got Fallout 3 only a few days ago and Gamestop had the GOTY Edition, although when I asked the guy behind the counter, he said they didn't. Proves he didn't know wtf he was talking about when I found 2 new copies later.
I didn't get the GOTY edition because of a buy 2 get 1 free deal and me and my wife didn't even go to Gamestop get Fallout, I had just been thinking about gettting it at the time. The GOTY Edition was new but the freebie game had to be a used one so I grabbed FO3 to see if I like it. I'll be going back soon enough to get it brand new and with all the DLC stuff.