I have not been able to find indication the sensor is bigger. In fact, the Apple Insider article below notes the same concern of more pixels in the same size space.
http://www.appleinsider.com/articles/10/06/30/iphone_4_review_3_camera_photosvideos.html
Looking at the comparisons above I am convinced of two things which have changed, and perhaps they are IOS4 related more than IP4. The exposure metering is different. The IP4 appears to use a center weighted metering, much better for P&S type of shooting where the 3Gs appears to use averaged metering. Look at some of the above images and you will see the same background brighter in the IP4 compared to the 3Gs. This is from the metering being based on the center of the image which is usually the subject at hand. This is a guess and I do not know this for fact but look at some of the shot comparison in the review below and perhaps you might think as I do.
http://carrypad.com/2010/06/25/iphone-4-vs-iphone-3gs-camera-test-video-and-photos/
I also think Apple changed their white balance calcs, as someone previously mentioned. The IP4 does seem to go a bit to the yellow side when shooting indoors when using tungsten. Seems like it isn't quite compensating as well as it could for the color of the light. Again, just a guess and something that can be fixed with a software update.
Just some thoughts.