I would say that the best thing to do is The Glow mission for the Brotherhood. Just make sure you take your Rad-X anti-radiation meds!
If you have at least one NPC to "mule" for you, there is a huge amount of expensive loot lying around there. You can cart it all back to the Hub and sell it to the various merchants. There's no point in keeping too many different heavy or energy weapons, just keep whatever you've got decent skill points in and sell the rest.
When I finished The Glow mission and uloaded the excess loot, money stopped mattering to me. I never had less than 30,000 caps and over 100 stim packs. I think I finished the game with over 40,000 caps because I ran out of things to buy.
Finishing the Glow has the added benifit of allowing you into the Brotherhood base so that you can get a hold of some Power Armor.

Wow! Great tip. I'll do the Glow mission now. :)

if you have over 50 on your gamble skill, you can sit at a casino and just hold down 1 and 4, and after about 30 min you'll have over 10k

Actually somewhere around the glow (at least for me it was) is also the truck special encounter. It's a pre-war wreck of a nuka-cola truck. You can figure out what you might find there :)

If you are short on caps, you can always do the pair of quests for Decker in the Hub. You find him by talking to Cain in the Maltese Falcon. I think you get 2000 caps for completing the first hit and 5000 caps for completing the second one. Besides, any time you can get paid to kill people from the Children of the Cathedral, it is a win / win situation.

I notice bodies dissapear with items, if you switch map areas. So I now loot and put stuff in a bookshelf, drawer, etc, and come back to them later. :)

I've come across this too, I hear tale they're supposed to decompose slowly after time. But for me, I've noticed the items are usually on the ground where the corpse was..