Is anyone else having signal strength problems on an iPhone 3GS since the iOS 4.1 upgrade?
Did you move from 4.0 to 4.1, or from 4.0.1/2 to 4.1? Between 4.0 and 4.0.1 Apple changed the calibration of the bar display, such that at a given signal strength it shows a fewer bars. They did that in response to the iPhone 4 antenna publicity, but the changes were done for all devices that support 4.x.

So, if you went straight from 4.0 to 4.1 getting fewer bars is expected, though if you are dropping calls where you previously didn't that is a real issue, or if you updated from 4.0.2.