There are many government agencies you could play with,
there is the;
National Geospatial-Intelligence Agency,
Office of Intelligence and Counterintelligence (under dept. of Energy),
Energy Information Administration,
National Nuclear Security Administration,
Lots of snacks under Office of Science (again, under dept. of Energy);
-Advanced Scientific Computing Research (ASCR)
-Biological and Environmental Research (BER)
-Basic Energy Sciences (BES)
-Fusion Energy Sciences (FES)
-High Energy Physics (HEP)
-Nuclear Physics (NP)
Defense Threat Reduction Agency,
Defense Logistics Agency,
Missile Defense Agency.
Many of which are obsolete after the great war (of course, even more obsolete than the others missile defence etc., so the enclave might stay away) and can be adapted to some falloutish stuff (mad scientist is kind of a cliché at this point I guess).
You also have some particle accelerators which could probably be adapted to some fun, if you had the energy for it. I imagine they would be quite unscathed from the nukes considering they are underground, at least they have some high power magnets and special components which could be of use.
I also imagined universities to be locations for some weird/interesting groups, but these of course all got nuked pretty bad.
For super weapons I would imagine High Energy Physics and Fusion Energy Sciences under Office of Science might have something interesting.
I just got this idea of a ridiculously unpractical weapon which would remove or weaken the earths magnetic field (either over an area or as a whole) so that everything under that area would get raped by cosmic radiation, sounds like something the reds would come up with during the 50's. It could be under some weird obscure agency, an agency that makes little sense, like the Office on Violence against Women got taken over right after the war by an insane feminist who developed it to kill men (maybe because her child died in the war?), however it makes little sense that the OVW would have scientists, so scratch that, but you get the general idea.