Obviously not the first to say this, but SPD/w mountain shoes. I just made the "switch" (thats one bike clipless-2 bikes clips and straps still) and I must say that I am very happy with them. they really make much more sense for commuting than say, Looks, which I have a pair of as well. The looks pedaled great, but one sided pedals are a pain in the A when you are in stop and go traffic, and you would NOT want to walk around a grocery store looking like a duck in them. With "old school" specialized mtn shoes, which look almost cool in my street clothes, I could almost forget I was wearing Bike shoes while running errands.

If you only have one bike, and most of your riding is going to be in proper shoes go with 2 sided, no platform SPD pedals, and use your spd shoes for "errands" You can buy cheap clip-in platforms for when you are taking your bike somewhere where you cant just wear the spd shoes, or just put 2 minutes aside to switch them out for some platform pedals.