Panniers are the ideal solution for reasons others have mentioned, except...

Most days I use a very small messenger bag (just about right for a jacket, gloves, pump, tools, etc.), just because it saves me the trouble of having to unhook and then carry the unwieldy bags with me, since I'm not willing to leave them unattended outside for 8 hours. If I want to pick something up at the grocery or just don't want the bag on my back because it's a warm summer day, I can always strap it onto the rack on my bike with a bungee cord. But if I'm planning to carry much (like winter clothing, a big load of groceries, something from the hardware store, etc.) the panniers are always the way to go.