I've been messing around with Media Control and finally am able to switch subtitles on and off using my remote.
I'm doing it thusly:
Late model FFDShow Tryouts, xvid and divx both set to libavcodec. Using ffmpeg-mt for H.264 but I think the important part is using FFDShow for everything.
Media Control remote control & keyboard configuration page set so Green button (not to be confused with Green Button) pulls up Audio/Subtitles page.
I've mapped the Green button to a "Subtitles" button on my Harmony remote.
Pressing that "Subtitles" button on the remote now lets me put a checkmark to show subtitles - seems to pull up the matching SRT or SUB file based on the show's filename. It also lets me choose other files, which is nice when I have different languages available.
Best part: The fantastic vroksub command line utility now works with OpenSubtitles.org's new API, so I have that running on my WHS box to automatically download English and Spanish subs for new programs as they come in.
I hope this helps someone. I'm loving it!