I honestly kind of hope New Vegas is the last Fallout game, and they just keep expanding it with DLC, patches and so forth. Anything Bethesda does will inevitably be a kick in the teeth, and Obsidian won't be able to rely on Fallout 1 and 2 references as much as in New Vegas.
Due to Obsidian's small size, I don't think we'll see them doing too many projects for Bethesda in the future. They're too independent to be tied down to one franchise/publisher/relationship for long, and after they're done with Dungeon Siege III, I wouldn't be surprised if the capital they receive from Fallout and that project allows them to more fully explore their own original ideas.
Ideally, we might see some sort of collaboration, with Obsidian providing help when it comes to things like writing and design work, Bethesda's larger team handling the core world-building, art and asset creation, and id Software providing either a game engine or some much-needed technical oversight to keep the project as bug-free and on-course as possible. Bethesda have some good qualities when it comes to design, but they need a proper focus and someone with a clear, rational mind to reign in and direct them properly, otherwise they end up with messes like Fallout 3.
Realistically, however, we'll probably just see Bethesda doing everything themselves, with the talents of both Obsidian and id Software going to waste. Bethesda fancy themselves world-class developers and I don't think they're humble enough to accept the fact that their games have problems others had solved over a decade ago.