I have found much useful information at this forum, so now it's time to bring my contribution. This is my first guide, so be nice...
I am using Plex mediacenter and want to have subtitles on my bluray rips. The problem is that there is no software at the moment which supports PGS subtitles, unless you want to try using svn or nightly builds etc. which does not always work.
To convert the subtitles from PGS to idx/sub in osx without the need for Windows, you need to download two applications. The first is mkvtoolnix >3.3.0 (http://jonthn.free.fr/MKVtoolnix/
) and the other is BDsup2sub.jar (http://forum.doom9.org/showthread.php?t=145277
Here is how to do it.
1. Open the mkv file in mkvtoolnix, and look for the subtitles. The line begines with "S_HDMV/PGS (ID x, type: subtitles)". You have to click on them to get the language. Remember the IDs for the subtitles you want to convert.
2. In the terminal, go to where your mkvs are saved and write "/Applications/Mkvtoolnix.app/Contents/MacOS/mkvextract tracks "the name of your mkv" "the subtitle ID":"the name of your mkv.sup".
3. When the subtitles have been extracted, close the terminal and open BDsup2sub.jar.
4. When you load the .sup subtitles, you will get a box where you only need to click ok. Now save the subtitles and use the name of your mkv again.
Now you will see the subtitles when you play the mkvs.