What it does : stresses CPU to it's maximum, allowing you to verify it's stability, and your cooling capacities. Based on Gromacs software used by F@H it's one of the most accurate stability tester for a machine aimed at Folding

How it works : it automatically detects the number of CPU's available in your system, and fully loads them.
This program is available for Windows, Linux and OSX, in 32 and 64bits version.
You can get it here : http://folding.stanford.edu/English/DownloadUtils#ntoc1
How to use it :
- start your monitoring software to keep an eye on the temperatures (CoreTemp or Everest are the most accurate for Windows, and lm-sensors is usually provided with Linux)
- start StressCPU v2
If it detects an error, the program will end with a message.
If your system is overclocked and unstable, you could also see a blue screen of death, or a reset of the machine.
There's no rule about how long you should run it ... but the longer, the better. There is an option (-t hh:mm:ss) to run the program for a limited period. If you don't add this option, it will run until it fails, or you press CTRL + C to manually end it.
NOTE : When you are testing your system, always let your cooling system stabilize. It will be fast with heatsinks and fans, and a bit slower on watercooling. It's the time needed for temperature to rise (in metal or water) and for your fan to spin at their optimal speed if they are controlled by temperature. It might be a good idea to set them at maximum speed while you're trying to overclock.
I hope this post is clearer enough and will help you test your machines ... feel free to post comments or suggestions

Mod Edit: Fixed Broken Link - PantherX