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[WINDOWS Only]
Attempting to convert a BluRay 1080p movie into MKV can be a bit of a daunting task. I seem to have figured out the easiest method as long as you don’t need to do any video or audio conversion. Any programs mentioned will require your own Googling to find, I will not post any download links.

1.) Open tsMuxerGUI and add the .m2ts file(s). Note, if it’s one .m2ts file, then just add. If it’s multiple .m2ts files you wish to join, add the first one, then join the others to it.
2.) In the tracks section, you should see all the files that make up the .m2ts. There may be many included language audio tracks, many included language subtitle tracks, but there usually is only one video track. Check/uncheck the files you wish to extract.
3.) Make sure you jot down each track’s current settings such as resolution, framerate, etc.
4.) For output, make sure you put the dot in DEMUX and then start demuxing.
5.) Once the files are split, you can then use MKVMerge GUI to merge the files into an MKV file.
6.) In MKVMerge, simply add the files you wish to put into the MKV container. Notice the tracks/chapters/tags it finds.
7.) Click on the video track and then edit the Format Specific Options to match the settings you recorded in #3 (resolution and frame rate especially, examples are 24000/1001 for 23.976fps and 1920×1080 for 1080p video).
8.) Click on the audio track and verify either the default Format Specific Options or alter to match what you recorded in #3.
9.) Subtitles will be discussed below, please read before running MKVMerge Muxing.
10.) Click Start Muxing and the file will be saved as .mkv which should be playable with Plex on Mac, XBMC, and VLC (though VLC has issues at the moment with very high def MKVs).

Subtitles
Subtitles from BluRay may be in .sup format. MKV does NOT support this format right now. Therefore you must convert it to one that it does support. The best I’ve found thus far is converting to VOBsub. A very nice program was written called BDSup2Sub which is a java program.

1.) Load the .sup into BDSup2Sub.
2.) Do not do any conversions unless you need to.
3.) Once loaded, export the subtitles as IDX/SUB (don’t check any boxes, just export).
4.) Then export the subtitles as IDX/SUB as FORCED only (save as a different file name from the one you saved in #3).
5.) In MKVMerge, add both IDX files (which will auto-add the SUBs upon muxing) to the list.
6.) “Forced Track Flag” refers to forcing a track to play always. Set this to “Yes” on the FORCED subtitle track. Set it to “No” on the ALL subtitle track. Set it to “No” for the video and audio tracks.
7.) “Default Track Flag” indicates which track for video, audio, and subtitles respectively will be the default one to play. This is usually only an issue when you have multiple video, audio, or subtitle tracks. In our case, we have 2 subtitle tracks. Set this to “Yes” on the FORCED subtitle track. Set it to “No” on the ALL subtitle track. Set this to “Default” for the video and audio tracks.
8.) Make sure the proper language is set for the subtitle tracks in MKVMerge.

That’s pretty much it.