I'm a rare breed in that I don't really NEED mods to play Fallout on my PC, but there are some I do tend to almost always have on.
For New Vegas I'd say Project Nevada, Nevada Skies, Rancho Villa, and DFB Random encounters are my biggest ones.
For FO3 I'd say MMM and Dynamic Weather are the main ones I'm always running. MMM is mainly for the respawning interiors and making the traveling merchants last longer. (They died too easy in the vanilla game, and go do so off screen.)