Vegan Essentials has a great footwear section, with quite a large selection.
There's always the fabulous Moo Shoes, based out of New York City.
Zappos has a lot of great shoes for every vegan foot.
My new favorite, Toms, has an entire vegan collection. These shoes are so cute!
Alternative Outfitters has many styles available.
Ahimsa specializes in Eco-Friendly, Vegan, and Sweatshop-Free shoes.
Pangea has a lot of great shoes on its website.
Bourgeois Boheme offers "fashion with compassion".
In Seattle, the Chocolate Shoebox is a great place to shop for chocolate and shoes.
If you live in Portland, check out these stores for great vegan choices:
My housemate ended up going to Herbivore Clothing Company (for those of you in Portland, it's located in the vegan mini mall) and buying shoes there. They are simple and they look comfortable, and it sounds like they were quite reasonable, too.