Best bulk domain registration?

godaddy probably would give you a good deal, talk to them maybe at first. They may give you better prices, if you tell them that you would buy them all at once.

If you need private whois you should go to namecheap as they offer it free for the first year.

There are several good domain hosting companies, among them are godaddy.com, iPage, and bluehost. There are still others you can choose from. You should talk with different companies and see which deal will work for you best.

Don't look at prices only - I would definitely go with namecheap, I've had domains with probably 6-7 different registrars, and namecheap are by far the best. You get free whois protection for a year, easy domain management, no jumping trough hoops when renewing, great support, and so on.

You could also explore becoming a domain reseller. Check if they have any objections to using the reseller account for registering your own domains.

Domain Name Prices @ Reseller Club

eNom - domain name, web site hosting, email, registration

I'd go with Namecheap and ask them what kind of bulk deal they can give you.

I have used namecheap in the past and they are on my NO NEVER AGAIN list. They are not an ICANN accredited registrar. They are actually a reseller for eNom, so when you do a whois it shows it's registered through namecheap AT eNom.
When you do anything there it has to get passed on to eNom and I experienced delays and failures of their interface with eNom. When you think you have paid to register a domain an namecheap, if somebody registers it elsewhere before they successfully pass the information to eNom, you are out of luck on the domain name, but they do give you a prompt refund.

As far as godaddy, just google "Mike Filsaime godaddy" and you'll get a couple of screenfulls of how godaddy will disable your domain for one complaint, even if unfounded.

My recommendation is name.com. I have been using them for about three years and never had any problems. I have used nodaddy, namecheap and netfirms in the past and now have my 50+ domains at name.com
When I checked their .com: $8.25 for transfers --- $9.25 for new and renewals they have a free privacy (forever so far) if you use a coupon code. "PRIVACYPLEASE"

Their domain management interface is the slickest and fastest I have seen, and they don't force you to ignore endless attempts at upsells

When you are buying anything there check at http://www.retailmenot.com/view/name.com for current discount codes. You cannot use 2 coupons in one transaction, so buy/renew a domain with a coupon and then go back immediately and get the whois privacy.

I heard moniker is pretty good for bulks as well but namecheap is an excellent option for most registration (just don't get into their redemption period; it's a LOT more expensive than most registrars @ $200/domain)

I'm down to 260 or so domains myself now (used to be over 1000 years ago) & use Moniker. However if I had 1000+ domains now I would "maybe" consider GoDaddy's Discount Domain Club - Discount Domain Club | Get the Lowest Domain Prices - GoDaddy