Last year I was diagnosed with fybromyalgia, which added another condition to my growing list of statistically improbable health issues. Of course one of the worst things you can do when you have any muscular problem is sit at a computer all day, as well as for most of the evening. Lucky I don't do a lot of that then! (ha)
Part of the problem is that moving around helps me to not get too sore, but if I'm concentrating on something (either at work or at home), I only remember to move around after I am sore, and by then it's too late to quickly reverse what's already happened.
I was recommended to try out some software to help remind me to get up from the desk and move around. Over the past 6 months I have been using Workrave. It is great, because in addition to accomplishing what I need it to do, it's free and open-source, so I can use it at work on Linux as well as at home on Windows.
Workrave can best be described as break-reminder software. I have it configured to remind me to have a "micro-break" every 20 minutes that I'm at the computer, and a "rest break" every hour.
For the micro-break, I mostly sit in my chair and do 30 seconds of stretching my arms, neck, and shoulders. For the rest break, I get up and walk up and down a few flights of stairs, or go to the kitchen and stand up for at least 5 minutes.
If I am diligent in following this routine, I have noticed that it significantly helps in warding off the pain.
One pro tip for using Workrave: by default it only counts down the time if you are actively doing something on the computer: e.g. either typing, or using the mouse. So if you are just looking at the screen reading something (which I do a lot as a technical writer), it doesn't count that as time. You can get around this by enabling "reading mode", which constantly counts down the time if the computer is unlocked.