Just to compliment my brothers posting earlier:
Not knowing the context under which you want to analyse this, and being very general I would suggest your first port of call is SPF or DomainKeys in order to limit the possibility of email coming from a rogue source being accepted. I would also recommend using only one SMTP server with SSL security. I do this and travelling worldwide I have rarely been in a situation I couldn't send mail and in those cases the only thing that did work was webmail (no safe local SMTP).
Additionally to that: if you are verifying mail is really coming from yourself then you could also use PGP tools to sign your mail upon sending and then filter any mail that didn't have a valid signature. Enigmail in Thunderbird is a good source of automatic signing and there are plugins for Outlook as well.
After that if you really want to do a more forensic job on an email then you could use a Spam Bayes to score the email against a database of previous emails. You would build up a database of tokens around the non-unique data (excluding entries such as "To:") and then score the email for the probability that it is like the previous emails. In theory you should score very highly for any mail.
Obviously I don't know your situation, but I think that there are many techniques but sometimes it is easier to go to the root of the issue than try and fix it down the line.
Update
Based on the context supplied:
I would consider using "Address Extensions" this is where your user can send mail to an address which contains a reference using the email address: [email protected]
GMail and many other servers support delivery of email with a +extension@ through to the correct [email protected] without hi-jinx. You could get the user to deliver mail with a unique ID as the extension and that way you would know it had come from them and they would feel more special. Obviously someone could steal their unique code by sniffing their outgoing or your incoming mail but that is always possible and if someone can do that they can probably inject mail as well.
If you really just want to go down the analysis route then I would suggest just using the reverse of a SpamAssassin per-user Bayes match. Where you compare every mail to a database of mails from a sender (instead of the traditional matching of mails 'to' an account). Remembering that once your database is polluted with a false positive you will have to remove the false positive or risk the integrity of the matching for that sender.