on Linux, there is a specification for supporting 'Media Player Remote Interfacing' [http://specifications.freedesktop.org/mpris-spec/latest/]. Very many Linux Media Player really adhere to this specification (e.g. vlc, banshee, rhythmbox). Sometimes, a plugin is needed, for example XMBC needs http://wiki.xbmc.org/index.php?title=Add-on:MPRIS_D-Bus_interface .
It would be very cool if Flirc would support MPRIS 2.2 on Linux. I guess that this would beak down to the following:
Provide a special keyboard layout in the Flirc application the could map the MPRIS functionality.
Provide a software daemon that translates the Flirc dongle (emulated) key strokes to MPRIS DBus events.