Pretty much everybody I know registered at Crate & Barrel or Williams-Sonoma. Some also had registries at Target, Macy's, and Pottery Barn. Jesse and I also registered at Restoration Hardware (and received nothing from that list). I have seen registries on Amazon and MyRegistry, which allow you to add items from many places on the web but are less convenient for brick and mortar shoppers. My point is: there are plenty of options out there, but here are a few more that you may not know about.
Garnet Hill: My love of Garnet Hill is no secret, but they didn't have a registry option back in 2010 when Jesse and I got married. Starting in 2011, Garnet Hill added a registry and I think it's a great way to stock up on high quality sheets or towels with fun patterns and colors (plus all sorts of other home decor items and organic lingerie, if you are so inclined).
L.L. Bean: Another registry unavailable when we got married but now open for business. If the L.L.Bean registry were an online option when we got married, we would have registered for flannel sheets, some monogrammed boat & tote bags, and possibly a kayak.
Anthropologie: Jaisa posted about an Anthro registry a while ago and I still think it's a great idea. This was available when we got married, but with his general anti-frilly nature, Jesse put the kibosh on that pretty quickly (I believe he asked the question "Where can we register for a dirtbike?" more than once). That being said, if you can get your partner to agree to an Anthro registry, go for it!
West Elm: West Elm is part of the Pottery Barn family, so it's no surprise that they have a "Wist List" option that serves as a registry. West Elm is a great option for reasonably priced furniture, rugs, and home accessories.
Any other ideas? Let us know and stay homey!