Every plex client (not DLNA clients) allows you to switch audio tracks on the preplay screen.
To know, which one is the commentary is a bit complicated atm.
As you can see in the first screenshot, plex does not tell you the 'title' tag you may have set in your MKV file for the audio stream.
Therefore I always order the audio tracks after the same scheme. First is always the regular audio and commentary tracks are always last. They are usually in a much lower bitrate or even mono so they are easily spotted.
You can apply the same logic to subtitles. Start with the forced ones, then the full subs, then the hearing impaired and last the commentary subtitles.
And a future version of plex brings a bonus which makes it a bit easier to select the right track: it displays the title attribute in the Media Info popup in Plex Web. (second screenshot)
To have several audio tracks and subtitle tracks in one file, you can only use MKV.
mkvmergeGUI allows you to reorder tracks by remuxing your mkv files. (This is much faster than pumping the file through handbrake or such.) You can easily set the 'title' tags and the 'forced' tag with it.
It is an essential tool for everyone who uses mkv.
