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How well does the .NET version work? I need to convert a bunch of VOB files/folders to MKV for the same reason (to use PLEX). Would this software be my best bet or is there another software that I should use? I have a ton of movies in VOB format, so I'd rather automate the process instead of doing ...

selecting the HD Audio only should be fine, you won't need the other 2...

Extras are usually all seperate video/audio files, so of course you will get a bunch of mkvs.... but if the files have the same specs (same codecs, same number of channels, same resolution) you can merge all of them to one ...

If audio quality is more important than disk space utilization, then rip the entire main HD audio track (and other same-language tracks if you like commentary, etc.).
This is the part I'm most concerned with right now. If I want the best for certain movies (action movies, for example) and I see ...

I'm a little confused on the different audio formats available when converting to MKV. Many movies (Avatar and 300 for example) have TrueHD or DTS-HD as a main audio section with DTS 3/2 +1 as a sub category below TrueHD/DTS. In addition, most movies will have another separate DTS 3.2 +1 that's ...