Here is my list of links to diaper sites that I have in my Favorites. I've only actually bought from a few of them, and I made a note next to these:
Wallypop - I have bought several diapers (as well as a baby carrier) from Wallypop. All her diapers are homemade and she is local. Great diapers, great customer service!
Little Padded Seats - This internet store just opened a shop in Valley Junction. They sell all kinds of diapers, and the owners are very nice and helpful.
Stork Wearhouse - Local!
Sew Crafty Baby - One of the few non-local places I have bought diapers from. Very good prices.
Jillians Drawers - They have a great cloth diaper trial that we used when we first started.
Pinstripes and Polkadots - not only do they sell diapers, but there is A LOT of great information about cloth diapering on this site.
Montana's Diaper Store
Jennifer's Cloth Diaper Boutique
Green Mountain Diapers
Soft Cloth Bunz
Cloth Baby Planet
Zany Zebra - this site also has a lot of great cloth diapering information!
If you have other sites that you have found helpful, please leave a link in the comments!