What you are asking is a very large piece of work. IBM themselves only document how to use Lotus Notes (5+) as an email server through JavaMail(there's a Red Book on their site somewhere if you have a search around which explains this in much more detail). You will notice if you look at the third party resources section of the JavaMail docs on Sun's site that there are all sorts of implementations of SMTP, IMAP and POP3 avaliable, but nothing which supports the non-SMTP compliant features of some email servers. I only know of one project which is even attempting this (mailsomething mail
http://mapi.sourceforge.net/) but it has yet to even release any code, so I wouldn't hold your breath.
However, your last topic suggested all you were looking for is a way to send email through a Notes 5 server using Java, correct? In which case JavaMail is fine, though you may need to either store more than 1 address against a user (both SMTP and Notes syntax) or write something to convert between Notes and SMTP. Remember that sending an email to a Notes server in the form
mailbox@domain.tld will work (because Notes is does have SMTP compliant functionality), you only have to worry about the difference between the addresses you have and those which JavaMail will allow.