Something I didn't realise at the start that seems so obvious in retrospect; all of the "inside" shops will generally buy what they sell, with the exception of the ammo trader. I.E. guns (in 30% or better condition) you can sell to the gun trader, armors to the armor, but more importantly; medical supplies, drugs and stealthboys can be traded to the basic medical supply for any caps he might have and obviously for the drugs and medical supplies you need.
The problem with doing this is you get only a small percentage of the items actual value (30% i think?) and at the end of the day, even if it is something you don't use it will be something somebody else does. So whether you want to just save items for player to player trades, or sell them for less than their worth is situational. For example i sold almost all of my stimpacks at one occasion when I saw the medical trader had 5000 caps in her inventory, that's about 10 A+ or S class missions worth of caps, but i got most of those stimpacks from doing vast amounts of missions in the past.
Assignments are easy and fun enough to do for a while, but after your 50th it becomes a bit of a chore to massacre poor farmers with superior firepower, so checking the traders for caps can prove less time consuming in the long run.