Peter Hosey, developer on the Adium X and Growl projects has dedicated a page on his website for applications that Apple killed.
This page lists every application that Apple has killed, along with the reason that they stated for doing so, and what has happened to the app since.
So far, the page only shows 10 rejected applications, including NetShare, I am Rich, MailWrangler, and Podcaster.
Contact Peter if you know of any other application that has been rejected by Apple.