Once again, thanks to John, I have done some upgrading to my setup as far as mail handling goes. I now have procmail filtering mail based on from address or subject and being deposited into different mailboxes. This works nicely for me, because mutt will cycle through my mailboxes, only showing me ones with new email, and this way I can prioritize them, so I see all of the security related emails first before I look at the junk. I had been using colors in mutt based on the sender, but was quickly running out of colors, even with groupings like friends, work, security, etc.
This change only took the modification of one line in my .muttrc and creating a .procmailrc in my home directory. Samples are pasted below.
.muttrc
mailboxes /var/spool/mail/user /home/user/mail/logcheck /home/user/mail/linux-sec /home/user/mail/gentoo
.procmailrc
MAILDIR=$HOME/mail
LOGFILE=$MAILDIR/log
# If you use EXMH, you might want to uncomment the following line
#MHCONTEXT=.exmhcontext # so EXMH sees the unseen sequence
# # safety net (commented out)
#:0c:
#$HOME/tmp_mail
:0 H
* .*securityfocus.*
$MAILDIR/linux-sec
:0 H
* ^From.*root
$MAILDIR/logcheck