I own the normal Retail Version of the game, registered to GFWL.
Now I want to buy the GOTY off Steam with all DLC during the xmas sale.
Will I be able to register it via GFWL? Is it just the basegame+dlc or is it an extra cdkey?
Is there any way to get the old retail deleted from GFWL?

1) it should come with it's own LIVE access key, & the retail GOTY only had one key in the case (don't know if different for the Steam version (aside from no case of course))
2) don't know but if you move your saves from where LIVE hides them to (C:\Users\yourusernamehere*\Documents\My Games\Fallout3\Saves) you can have your saves offline. though Steam most likely will install the GOTY as a separate game.