Whats the best way to earn caps? In New Vegas i had no problem getting 100,000 + caps. In FO3 I've only managed about 9,500 caps. Help?

Its normal to have that much in Fo3 dont ask why

They are different games. example : The combat armor's value is 390 in FO3 and 6500 (!) in new Vegas. And the vendortron can easily have 12000 caps to buy things when Flak and shrapnell will never have more than 1600.
The capial wasteland is ruined, poor and primitive, the west is rich, with trading companies and organised business.
Like in real life, depending of where you live the same amount of money makes you rich or poor.

You know the joke about the United Nation survey :

Last month, a world survey was conducted by the UN. The only question asked was: "Would you please give your honest opinion about solutions to the food shortage in the rest of the world." The survey was a huge failure...

In Africa they didn't know what "food" meant.
In Eastern Europe they didn't know what "honest" meant.
In Western Europe they didn't know what "shortage" meant.
In China they didn't know what "opinion" meant.
In the Middle East they didn't know what "solution" meant.
In South America they didn't know what "please" meant, and
In the USA they didn't know what "the rest of the world" meant.

In my game, I work hard to NOT receive caps. Trust me, soon you'll be rolling in caps. Most characters I fielded pre- my new system of playing FO3 often would have 90K+ caps at about level 30.

First, find all the vendors and then get into the caravan thing. Then just kill stuff and sell the loot. Get a companion, or two or three with mods, to help carry it all. Save it up in Megaton and then go on a tour of the vendors selling the items. Then repeat ever three days after their inventories reset. There are about 12 pretty good vendors (if you don’t kill them first) plus the caravans.

After the Enclave start up, there will be much more loot than there are caps to buy it, so I just take the rest out as ammo and aids. I played one of my characters a while today and she just sold a ton of stuff and now has a total of 247, 847 caps. Not that there’s anything she can do with all that, but that’s what she carries around.

I think the reason you're having trouble in FO3 compared to FONV is that in FO3 the value of somethings are super deflated and others are not compared to NV. For example, one (1) 5.56 round is worth one (1) cap in both games. One (1) stimpack is worth 25 caps in FO3, 75 in NV. Minigun is worth 1,000 caps in FO3, 8,000 in NV. In Fallout 3 you are paying the same price as you did in NV for necessery items like ammo, but you are getting on average 1/5 the caps you would get in NV from selling loot.

Of course in Fallout 3 you can slaughter any unnamed NPC you want since their is no faction reputation, so kill as many BoS troops as you want. Power Armor sells well.