I think the first thing you should do is decide whether you need to be able to walk around in your bicycling shoes. Road bike shoes tend to have slick, treadless soles and large cleats; walking in them is a challenge. Mountain bike shoes tend to have recessed cleats; walking in them is easy.

I tend to do longer rides and I like the flexibility to get off the bike and walk around during a break. Skating around on slippery road pedals always made me nervous, so when it came time to buy pedals for my new bike I bought mountain bike pedals. I chose Crank Brothers Eggbeater C pedals; around $45 shipped to my door. For shoes, I chose Shimano MT31s. They have a very stiff sole but look enough like a regular shoe that nobody will know they're cycling-specific; great for commuting.

If I had it to do over again, I might try the Crank Brothers Smarty or Candy pedals. The small platfroms on those pedals might make it easier to pedal the bike on the rare instances where it takes more than one try to get clipped in.