waterproof zippers
place to hang a light or reflector straps
reflective trim
padded laptop sleeve that keeps the laptop off the ground/suspended when you put the bag down.
velcro & buckles
well padded strap, especially in large size bags that can take 30 lbs of junk
y strap that can connect to either side
organizational pockets in addition to large main compartment
nice if you can access a side pocket while the bag is in place

I have two patagonia ones
their first critical mass bag from about 01 - probably have 10 thousand commutes with it.
just got their smaller version (3rd gen) which I like a lot too.

lifetime warranty and quality construction. love their gear.
www.patagonia.com