I like Gandi.net. A bit more expensive at $15.50 for a .com, but it includes DNS, SSL, web redirection, and email (nice for setting up forwarding addresses).
Even those without domains to move can also do something useful, Convert any links to GoDaddy that you may have to plaintext. This also boosts your remaining links :D
While at it, convert all links you may have to crummy places to plaintext.
I personally use https://www.inwx.de/en
They have an API, provide nameservers, are comparatively cheap (at least for the TLDs I own) and have a nice minimalistic interface targeted at professional users
I've been using www.dyn.com for years and would happily recommend them. Not the cheapest but they are a lovely company to deal with (and are probably one of the most hardcore DNS providers in the world - Twitter offloads their DNS to them for example).
I have been using nearlyfreespeech.net for several years now, and it has been just about perfect for my needs. If your site will have low traffic, or if you want just registration and DNS, then I would highly recommend NearlyFreeSpeech
Just a few days ago, I was about to move to namecheap but then I find out their interface was a little too simple. It was missing more advanced features that even godaddy has like import/export zones. Looking for other suggestions too.
I just transferred all my domains from GoDaddy a few weeks ago and Hover made it simple, got it all done within a few hours. Had some trouble with a subdomain and a custom landing page and Hover's support was very helpful in helping me rectify the issue.
I looked into Lift. Steep learning curve. It would be ok for a single person, but a large team coming up to speed on Lift/Scala looks hard. Then I decided to stick with what I know best Ruby/Javascript/Node.
Thanks!