Funny this was pointed out. I've have the same Frogz case on my 3G s as I had on the 2G and I find it warmer. I hoping this isn't a problem when I spend time outside in hotter weather.
If you disable your wifi can you still get online through the cellular network? I couldn't on mine until i fixed my APN settings. The phone was constantly trying to connect and it was eating up the battery life.
To avoid the battery drain, turn off push notifications and wifi. I don't think that affects the warm issue as it stays pretty hot anyway. For wifi, make sure to reset your settings on the phone because after doing the 3.0 update the phone will supposadly be trying to connect to the net constantly. The reset of the network settings may stops this.
I went to Best Buy and bought a silicon case for the phone. It dissipates alot of the heat. Highly recommended if the heat issue is really bugging you.