The functionality to apply filters to recordings already exists in the transcoders profiles, but currently this method is not very user friendly (its just an argument string). Filters can also be applied in the same way on a per channel basis during recording or playback. There is some discussion on the developer mailing list of adding a GUI for filters in the future, but nothing recent. Section 10.4 in the user manual describes the currently available filters.
This would be similar to the Recording Profiles setup screen that would contain a list of applied filters and an (add new filter) item at the bottom. Pressing the menu key would bring up a menu with the options to move the selected filter up in the list (to be applied earlier in the chain), down in the list, or to remove it. Selecting (add new filter) would bring up a new screen with a list of the available filters. Each of these items would then bring up a wizard to walk the user through inputing the required parameters of the filter. Selecting an existing filter brings up the wizard for that filter to alter the values.