When I do it, I use the "workrave" program under Linux. You can set your times and it shows you when you need to give a break. It also shows some exercises during breaks.
It's pretty awesome. I have it set up to lock my computer without any way (besides going to the tty screens) to unlock it... Any other way and I end up postponing the breaks and not taking them.
Arg! I have this same problem. I typically end up killing it at one of the ttys at some point during the day.