The one thing I'm positive that you don't have before paying $99 is access to beta SDK downloads and supporting documentation.
In years past Apple has released materials from Apple's World Wide Developer's Conference (WWDC) to the paid site but not the general area. I don't know what they're doing now.
As far as the other poster's comments, I'm not sure what documentation and sample code is only for paid developers.
It's a bit hard to tell without a painstaking comparison. The developer site looks different when you are logged in vs when you aren't, so it would mean taking detailed notes of both versions - which is something I don't really have time for.