Bob O'Neill left an App Store comment and points out that the iPhone has a tendency to heat up if SrutiBox is left on for a long time. This is probably due to the intense computation the phone is doing while synthesizing the tone. All you have to do is stop the program - you don't have to de-install SrutiBox to make it cool down. It works for me that way.

Version 1.1 is actually a lot "cooler" than the old version - if a reed has zero volume, (or is "off") it no longer tries to compute it, so it doesn't have to go through all those cycles. SrutiBox now runs at about 16KHz instead of 11KHz, so running it will all oscillators going is going to give it a lot of work to do.

other things to look for :
http://forums.macrumors.com/showthread.php?t=329120 says:
Most likely culprit of your heat problem is WiFi and auto-connect for WiFi. Turn both off. It will improve your battery life A LOT and it won't run hot... or it shouldn't.

I'm always running WiFi, so that might be a contributing factor.

That being said, I'm looking forward to having a pocket hand warmer around this winter - that you can call the gas company on!