Generally I set up shopping systems to apply tax only when the customer is in the same state as the business. For example, I'm working on a couple of sites for businesses located in Virginia, which has a 4.5% state sales tax. So when I set up the carts I have the code checking the shipping address, and if it's in Virginia then the sales tax is added. With a state like California which does per-county tax I imagine it'd be a bit harder to script properly, but the same principle should work.
I also make sure that there's a prominent notice informing customers of this: the price listings all have a note attached stating "Virginia residents will be assessed an additional 4.5% sales tax."