Any game with editor, ever since Doom and even before. Most popular games have editors even if not official ones that let you create about everything possible within the context of the game.
But if you wish I can name few just off the hat:
D:OS 1 (and 2 when released)
Forementioned Doom
Duke Nukem 3D
Shadowrun
Far Cry
Crysis
Neverwinter Night 1&2
Diablo 1 & 2
The list could go on practically forever. There's nothing specifically unique in Bethesda in this regard, outside of popularity of modding to that game.
Do you have issues with reading? WoW has nicely functional world editor (In fact, many editors) that lets you either work with existing stuff, or create entire continents from scratch.
https://www.youtube.com/playlist?lis...eature=mh_lolz
This one is my favourite as it's very simple and you can have entire zones outlayed within minutes.
Fallout 3 problems have quite little to do with bugs and more with the game itself.
Patently false. The ES serie used to have robust faction system where choosing what factions to join actually affected the game and disposition of the characters towards you. Hell, Morrowind in some guilds and factions you go and directly destroy the opposing one, or at least their leader. Also you can only join only one Great House.