You join the Made for iPod and Works with iPhone Licensing Program - it involves a few NDAs and legal documents, then they give you the specifications for connecting with and communicating through the i/o port or bluetooth.
Here's a blog post detailing what one person went through to get into this program and gain access to the documentation:
Part 1:
http://www.stackoverthrow.com/?p=97
Part 2:
http://www.stackoverthrow.com/?p=100
It looks like there's no extra fee (above the usual $99 developer program fee) but there's a lot of back and forth paperwork, including faxes, mail, etc which stretched the process out for him to nearly 2.5 months.
He hasn't given much of the nitty-gritty details, so there may be more to it (ie, you may have to disclose your intended application, and if they don't like it they may turn you down) but it gives the process from a recent program applicant. Would be nice if it changed so it was all online, but I'm thinking they may still require all the paperwork.