Our web-based email client BearMail now allows for the configuration of server-side email filtering.
Rather than filtering your mail when you check it (Thunderbird, Apple's Mail, and other desktop clients), mail is filtered into sub-folders at time of delivery. The main advantage for users is that filters are stored centrally on the server, and there is no longer a need to duplicate them on all clients used to check email.
In general, if configuring server-side filters using BearMail, it is best to delete all filters in your email client. This will reduce the likelihood of complications between filtering done on the server and filtering done by the client.
Also, your mail client may need to be instructed to check sub-folders for new messages. Thunderbird is a known client where this needs to be done, while Apple's Mail client in OS X/iPod Touch/iPhone needs no additional configuration.
To get started, log in to BearMail and click Filters at the top of the web page.