Well I've only ever had experience with RegisterFly and NameCheap.
RegisterFly: I have most of my domains with them and on the whole haven't had any real problems. Their prices are good though and they have a wide selection of TLDs and ccTLDs. I'm not a fan of their current interface although I've been told this is changing soon, so I'm hopeful. Another benefit I suppose is that RegisterFly is ICANN accredited, meaning they're no longer a reseller for another company. Also there is a RF employee on the WHT forums which is great if you ever need to contact support as otherwise you'll end up waiting a long time for a reply which doesn't say much.
NameCheap: I've only a few domains with NameCheap which I only registered there because RF suspended my account for three or so days. Their prices are good and their interface is simple and quick to load which is exactly what I want. They're smaller than RF and are still an eNom reseller, although I think this is actually an advantage since they don't have the growing pains that RF are going through. I've not had to use support so I can't say.
I'll still use NC from time to time, although overall I'll stick with RF and may even in the end transfer my domains from NC to RF.