My iPhone battery gets hot occasionally so, of course, I googled it. It turns out that, despite Apple’s restrictions on third-party applications that prevent them from running in the background, they aren’t preventing problems from their own applications.
The standard iPhone apps like Safari, Mail, iPod, Youtube, Stocks, etc do not neccessarily close themselves when you hit the Home button. You need to hold the button down for 8-10 seconds while in the application to force it to quit. Umm, okay.
An alternative is to shut down your iPhone a few times a week. (Hold down the power button till you get a screen asking if you want to power down.)
Heat really reduces battery life so this is definitely worth keeping an eye on and powering down whenever it starts overheating.