I forget, have you picked out pedals yet? That's going to restrict your shoe choices somewhat.
You have two, possibly 3 broad options: 2-bolt cleats (Shimano SPDs and Crank Brothers, essentially), and 3-bolt (Look-style; also includes Shimano SPD-SL and Time) cleats. There's also Speedplay that makes a cleat/pedal system that requires 4 bolts, but there are adapters for 3-bolt shoes out there. Flip the shoe over to see which it'll work with. There will be either 2 long holes toward where the ball of your foot would go, or three holes arranged in a triangle near the toes. There are advantages and disadvantages to each.
2-bolt cleats go with pedal systems that are designed primarily for mountain biking. The pedals are near indestructible (I recently came into possession of a pair that's at least 10 years old and works beautifully), and the cleats are designed to shed mud. The fact that they're designed for mountain biking means that the cleat is recessed into the shoe. Basically, you can walk in them far more easily than you can in "road" shoes. The downside is that the contact area tends to be much smaller, and this can put pressure on your feet, resulting in hot spots or numbness. You can find SPD pedals with a platform around the mechanism, though.
Road (3-bolt compatible) shoes are harder to walk in because the cleat comes in contact with the ground, so the cleats will wear and you'll slide all over the place if you visit a convenience store. (Ask my BF how I know!) They do sell rubberized cleat covers to help with both issues. The contact area is larger so there is less pressure on your feet. For long distances, these are generally the better choice, though there are many on here who ride long distances with SPD pedals.
As far as shoes go: Fit, fit, fit, fit, fit. Go try them on if at all possible. For long distances, you want a fairly stiff sole and proper foot support. The shoe should fit more snugly than running shoes, but you should still have plenty of wiggle room. Try them on at the end of the day, because your feet swell during the day and with exercise. Make sure your heels don't slip. I'd invest at least $100 for shoes, because that's one of the three places you come into contact with the bike. If you've got a Performance near you, I believe all their shoes are on sale right now--they carry some Mavic shoes that are really comfortable. (I think the one I tried was the Avenir. I was sad that it didn't quite fit in the heel.) Specialized also makes some nice shoes if they fit your feet. They seem to run a little big and wide in the heel, though.
Pearl Izumi makes nice stuff, though I've never tried that particular shoe. I can't see how they're compatible with both pedal types; I see only one set of holes in the picture.