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You might be able to just enable the comskip plugin in the tv-server configuration.  Then setup a little batch file with your mencoder command line and you should be able to use {0} as the input file since it's being passed to comskip (or so the tv-server thinks).  Then just set the batch file as the location of comskip.

That should theoretically work I would think.  Of course, there may be a completely different and better way to do it, but this seems like the quickest/easiest.