I use Dreamhost for all my domain registrations and most DNS. Great admin interface compared to the competition, still very cheap, domain transfer codes plainly visible, no unlocking or calling or any of that. You just transfer it away. They are the most honest of the bunch and you can move each part of your service off them as you outgrow it.
Easiest to setup a domain for Google Apps too, just click a button.
I immediately transferred to Moniker - they're great, they let you configure absolutely everything. I think what I learned was to stay away from companies that do both domains and hosting. If they just do domains, they understand that you are always going to be sending your traffic elsewhere.
I use GoDaddy because I manually renew all my domains at the same price as I signed up for. I agree their UX is awful, and they're not the most "good" company in the world... but it serves me for what I want out of a domain provider!
Renewal price hiking is a common practice... you just need to be a smart shopper if you want to save money!
I'd really like to switch, but one of these alternatives are going to need to really compete on price.
If you're not hosting with them, then you're doing it right.
I may have said it elsewhere, but I'm a big fan of DirectNIC even though they are double GoDaddy's price. There interfaces are really clean, and any time I've transferred or sold a domain it has been an absolute breeze. And back in the day, when all the major registrars were shutting down their web-based WHOIS tools (NetSol et al), DirectNIC always kept their WHOIS tool open which always bought them a lot of good will in my book. (I wasn't aware of command line tools like 'whois' and 'nslookup' yet...)
http://online.wsj.com/article/SB1000142405270230458400457642...
Reasons why I wouldn't use GoDaddy:
GoDaddy is not really one of the cheapest registrars.
I find their pricing "tactics" (as also mentioned in the article) very questionable.
Their whole website isn't just really appealing to me (I know, very subjective).