For me, here's my list of pro's and con's:

Backpack Pro's:
1. Easier and quicker (to pack and to take with me)
2. Better weight distribution
3. No modifications to bike - can use regular road bike
4. Lighter
5. Cheaper
6. Keeps my back warm in cool weather
7. Less wind resistance

Pannier Pros
1. Hold more stuff for winter commuting
2. Not hot on my back in cold weather
3. Easier to see behind me with my helmet mounted mirror
4. Generally more waterproof
5. Less weight on my saddle (had saddle sore problems)
6. Rack gives nice place to mount a light