Is it possible to schedule running Mail.app rules?
Here is how I would approach this - note it is quite technical and is recommended only to people who know what they are doing.

1) Write an Apple Script to send the keystroke to apply your defined rules in Mail.app

2) Schedule a crontab to run that script at predetermined times

To start you off here is a sample script that I have written:

tell application "System Events"
tell application "Mail" to activate
keystroke "l" using {command down, option down}
end tell


Then to schedule your job (e.g. midnight) by adding a crontab entry - change the username to the user you are running Mail.app as - leave osascript as it is

* 0 * * * username osascript 'path to your script.scpt'

Alternatively use a GUI to schedule the above such as cronnix http://code.google.com/p/cronnix/