I have a site-wide SpamAssassin configuration. In addition to this, I use ClamAV-based site-wide virus filtering.
Each of these systems tag messages with additional headers before delivering into /var/mail/user. So it would be nice to filter out mail flagged as spam from the rest of your new mail before reading.
I use Sieve (specifically, the implementation in GNU Mailutils) instead of the dreaded procmail to filter my mail from the mail spool into various folders.
My Sieve configuration, in addition to checking for SpamAssassin and ClamAV flags, has an additional layer of heuristic spam-checking that I'm constantly evolving. You might find it to come in handy!