Depends on lifestyle, commute distance and physical strength and weather.
I have commuted for about 10 years now (Can hardly believe it myself). I am now using the courier bag, a Timbuk2 one. I have used everything from paniers to backpacks to courier bag.
Why do I recommend the courier bag.
You can fit more into it, it is more flexbile and it has pockets for all the nice bits and pieces, a key holder, place for your wallet, tools etc. It is also the only way I could easily bring my work stuff and my change of clothes around.
I did not find the backpack great, I also did not find paniers great as I use a Sirrus and the weight all on the back was too much then installled low loaders and used these for two years with Ortlieb paniers on the fornt. Pain in the ass balancing weights each day, bought the courier bag, never looked back. Using it now for 18 months 5 days a week plus holidays, weekends away etc.
HOWEVER, I live in Dublin, Ireland, while we get rain and cold (no snow) we do not get really hot weather. If we got really hot weather then I may be singing a different tune
Hope this is of some use to you. No right or wrong answer on this one...