Mark has many blog posts about this, and here are two of my favorites:
16 Tips for Desk Jockeys: What to Do About Sitting All Day | Mark's Daily Apple
10 Ways to Make Your Workplace Healthier and More Productive | Mark's Daily Apple
I personally do stretching on a regular basis while sitting at my desk. During lunch, I go for walks. Sometimes, if I'm not feeling self-conscious about it, I do squats or simple standing yoga poses in my cubicle, too.