The Graphic Artists Guild has an Ethical Guidelines and Pricing Book that is considered widely as the standard for this sort of thing.
You will have to evaluate how much time you spent, how much your talent is worth, and decide how little you will settle for(since somebody is always ready to undercut your price). Personally, I think that the 3D you created is worth far more than the site itself, and the client should be gently informed of that. The site itself could have been pretty easily put together in a couple of evenings. The 3d, no doubt, took up quite a bit more of your time. (If I’m wrong, please forgive my assumptions). Anyway, the point is, if you want more money, you have to find a way to explain to the client why it is worth more…in your case, the 3d is what makes you the person for the job as opposed to some 12 year-old with a mac and flash (who would probably build a cheesy site for 200USD).
I would also recommend locking in at least a ballpark price before your next project begins–in writing. If you trust the person enough to work for them without a contract, you should still probably have already explained the amount of work to them, and agreed on the price.
Good Luck,
Dain