Just a quick note, because I had to dig to find this feature out. I use the program called Workrave, as an anti-repetitive stress injury program. Works pretty well. Best one I've found so far.
It's fairly configurable, but it won't save your configurations to a specific file without an extra step. So if you reinstall your OS, you have to manually configure it again.
After digging through their docs, I found you need to create an empty workrave.ini file in your ~/.workrave directory. Simple huh?
Now I can take that config file and move it around to other machines if need be.