I guess it depends a little on how the hood is cut. Some jackets have a hood that's big enough to go over a helmet. I have a ski shell that will probably start doing double duty as a a commute jacket once it gets colder. The hood is cut to accomodate a ski helmet, but I need to experiment with this. If the helmet doesn't work, I'll probably go with a helmet cover, or maybe one of those cute Gore-tex cycling caps that Terry sells

I highly recommend fenders if you don't have them already and your bike has eyelets for them. Even during the summer, fenders keep a lot of spray from standing water and road muck off of your legs and bike.