I've researched the different honeymoon registries quite thoroughly and I'd love to save a fellow bride some time!
www.honeymoonwishes.com and www.honeyluna.com are the best ones I found. Honey Luna has travel experts to help you plan your travel. Your site is free if you go through them. Either site is easy to use, allows you to take out money as frequently as you wish and you can share details, photos and more with your guest list.
If you use one of the "partner" registries you can have the gift of massage, upgrade, etc. go directly to the hotel. It's really up to you! Honeymoon Wishes and Honey Luna offer the most flexibility and professional service.
I'd steer clear of Honey Fund. It's really more of an IOU than anything. Plus, they sell ad space on your webpage, etc! Yuck!