I'm now back from having several weeks rest after a major operation on my neck to replace a slipped disc with a Titanium one. The operation went well, I just need to now focus on doing a lot of regular neck exercises through the day to keep me from seizing up.
Thankfully I found a neat little application called WorkRave. WorkRave is designed to help stop repetitive strain injury (RSI), but I've been using it to tell me when to have short breaks to exercise my neck and back.
To install it on a Ubuntu system use:
sudo apt-get install workrave
WorkRave allows one to configure short micro-breaks, rest breaks and daily work limits. At the break intervals, one is presented a set of short exercises, such neck turning, shoulder-arm stretches, should movements, neck tilts, etc...
I'd recommend using this application if you need regular desk-exercise and don't mind a little bit of regular nagging from the computer. Give it a try! It's certainly helped me!