If I have to, I go with a pack over a messenger bag - just feels more secure to me. But as others have mentioned, it can affect your posture and cause back pain. I can also make you sweat like a pig. I commute into Boston, MA (5 miles each way), and even in cooler weather my day hike pack, which has ventilation channels built into the back panel, can soak my back.

You can find some pretty inexpensive bike panniers on ebay. Add them to a cheaper rack or other support, and it may just run you less than a decent commuter bag or backpack.