While Apple has yet to deny or confirm, a few owners of the new iPhone 3GS have complained about the device heating up, even to the point of warping the plastic and discoloring the white-backed phones. There have been problems with batteries in Apple devices before (Sony-made batteries, to be specific).
I currently own an iPod Touch (1st gen) with 16 GB on board, and even when the original turned into a brick following the original 2.0 software upgrade, Apple made good with a new device at no cost. But now there’s some suggestion that the 3GS may not be having a battery problem; 2nd gen owners of the iPod Touch have noticed a shortened battery life and hotter device since upgrading to the iPhone 3.0 software upgrade (that same one that iTunes keeps begging me to spend $10 on every time I sync up).
Recommendation: Sound an awful lot like a power management issue. I’d hold off on both for just a while if you have or want an iPhone.
Kevin A. Ranson : ThinkingSkull.com 
No problems yet on my iPhone 3gs. Knock on wood.
(sent from iPhone 3gs)
According to Wired:
http://www.wired.com/gadgetlab/2009/07/iphone3gs-battery-test/
Demonstrating that the iPhone 3GS did have better battery life compared to a new 3G (and that an nearly year-old 3G had only lost about a fifth of its battery capacity), it’s now looking as though there may be a few defective batteries out there rather than a design flaw or firmware issue.
Of course, there’s still this:
http://www.wired.com/gadgetlab/2009/07/slow-chip-iphone3gs/