I know quite a few people have been having problems with subtitles in TVersity Media Server.  I seem to have found the problem and fixed it.  It is a two part fix, and is not the ideal solution as it is not always automatic and requires some doing.  However if you have a large collection of things with subtitle this can make it usable.  The first thing to do is to launch some of the files in question and see which decoder tray icons show up.  Usually you will see FFDshow audio and video decoders, Hali Media Splitter, and sometimes Direct Vob Sub.  Start by configuring the FFDshow video decoder checkmark the subtitles sections, and then select Vob Sub section underneath that and select two perferred languages.  Next go to the FFDshow VFW Interface and repeat the same process again.  Next open Hali Media Splitter configuration and select the options tab.  From there expand the section entitled Languages section and add appropriate values to all the sections there.  The options and method for entering these values is shown if you hover the mouse over each section.  This is very important to the process so make sure it is done right using the proper 3 letter language code, commas, and semicolons where appropriate.  With that done some of your subtitled media may start working, however most won't particularly embedded MKV file subs.  To get the MKV subs to work we need to make a directory on the harddrive in which we will put subtitle files, now go back to the subtitles section in both the FFDshow VFW Interface configuration, and the FFDshow Video Decoder configuration.  In both configuration section we need to configure the main subtitle section where it says "Search in" and point it to the directory made for the subtitle files.  Now here comes the real pain in the butt.  We now have to use a program to pull out the subtitle files and put them into our subtitle directory.  I use either MKVextract or OGMcleaver, MKVextract works very well.  I usually pull all the subtitle tracks, and the embedded fonts and put them right into the subtitle directory.  Now if everything went right you should have your subtitles back.  Hope this helps, so far it seems to be the only way to get most of your subtitles working.  As for OGG files I have not yet found a way to make these work yet.  However I don't see many OGG files these days anyway.