Does anyone know of a JavaMail API implementation for Lotus Notes R5?

Since the mailbox in lotus notes is just a notes database, you could use the Notes Java API supplied by lotus.
Check out: http://www.lotus.com/developers/devbase.nsf/homedata/homejava.

Also, Chandra Patni reports that Lotus supports imap protocol. So you can use the basic JavaMail API for Lotus.