Without more detailed information which applications you use and exactly how the data for your users is being stored me. nor anybody else will be able to to give you an optimal suggestion
Actually you should be able to get that info from your current server.
According to the FreeBSD
hier(7) man page, programs installed from the ports system are installed in
/usr/local. So by creating a separate filesystem for
/usr/local you will separate your applications from the remainder of the system.
Rationale: a problematic port upgrade from one of your applications can now be easily fixed by restoring the previous version from backup.
If your data for your 10000 users is being stored in MySQL tables/databases somewhere under
/var, then create a separate partition for those tables. Same for the mail.
Rationale: you don't want a massive spam attack (delivered to
/var/mail) completely fill up your
/var partition and thus denying your users to store their data in your MySQL databases located in the same
/var partition. Or the other way around