The first site that really stuck out to me in exploring cloth diapers was cottonbabies.com. They are the manufacturer of bumGenius diapers. I'd heard lots of great reviews on the bG diapers, and they're a relatively local manufacturer. They have a How-To section that was very helpful to me.
The Diaper Pin is a great site to get cloth diaper reviews. Early in my research I found this helpful when deciding on the brands and stores I wanted to use.
Recently, I've found DiaperSwappers.com to be a useful site when it comes to getting advice and tips from other moms "in the trenches," trying to figure out how to diaper their own children successfully and easily.
I have really appreciated the quality and quantity of information presented over at Pinstripes and Polkadots. There's a lot of great reading there, and bonus for me, also a kind-of close retailer.
In terms of places from which I've purchased, most of my diaper purchases have been through Cottonbabies.com. Since they are based in my home state, I like that I'm purchasing from a business that is "local" to me. They've also treated me well with great customer service.
I got my organic prefolds through greenmountaindiapers.com. They have a great selection of natural fiber diapers, and I've read great reviews on the quality of the diapers. So far, my red-edge organic prefolds have held up well for 2 kids and 2 years.
Nicki's Diapers has a great selection and prices. I've also purchase reusable swim diapers through the sister site, myswimbaby.com.
I've purchased a few times through DiaperJunction.com, before it was purchased by the current owner. It looks like the selection has grown, and I've read good reviews about them in recent years.
Disclaimer: I don't sell or make cloth diapers for anyone, I am not affiliated with any cloth diaper business, and I have received no compensation for posting about these sites