Here's a few ideas to toss around concerning the topic of warming up.
First of all, I've found that doing stretches AWAY from the guitar (as seen on the Rock Discipline Dvd by John Petrucci) is an invaluable way to begin. Streching out the muscles in the arms, back, shoulders and even THUMB allows me to feel as though I've already been playing for a half hour or so. I promise you that if you give this a try for a week, you'll never start any other way. You'll love the increased sense of relaxation and flexibility.
For those players who are still relatively new to the instrument (or those who don't yet have this down), I'd use this time to learn a new scale or arpeggio. Since warming up is meant to be a time that you play SLOWLY and just get the fingers moving around a bit, learning a new scale is an ideal point of focus. You'll not only retain the info better (since you are "fresh"), but you'll also likely get use of every finger...2 birds, 1 stone.
I really can't stress this next point enough, since it's the key to speed, flexibility and injury prevention: RELAXATION. When you are starting to move those fingers around, focus on using a light touch right from the start. Also, pick lightly at first; you can always pick harder after the warm up. You don't lift 100 lbs before you lift 50 lbs.
The last idea is sort of an indirect one. Warm up your inspiration! While doing some stretching, throw a video of one of your favourite players on. Get inspired! This always gets me primed for a practice session. I tend to focus better and get new ideas along the way. Now if Chris will only release that damn DVD.....
Kel