For commuting I'm fine with my backpack - I might end up getting a grocery-pannier that I can toss my backpack into for a cheap solution, as most of the messenger/backpack-panniers I find are pretty expensive. My commute is only 5k each way, and I shower at the gym before heading into the office anyways - so getting a bit sweaty isn't that much of an issue.

For recreational rides / training rides - I prefer my rack-top bag. It doesn't get in the way taking it onto elevators/escalators/etc, removes easily, converts into a small back-pack if needed, and big enough to hold a few layers / tools / snacks / drinks. The weight of my backpack starts to get bothersome after anything longer than a few K.