Unless you have a multichannel audio system I would suggest a profile that re-encodes the audio (like h264+aac), the file will be smaller and the video will look just as good.
I am sorry Signals but I disagree. (I don't see the MKV container listed?)
I feel the best way to future proof your files is to retain multiple audio tracks.. The price you pay is a slightly larger file but means that you never have to go back and re-encode if you change your equipment. With the cost of hard disk space these days, the impact is minimal.
AAC as the first track to retain iCrap compatability (unfortunately as I hate Apple Crap)
Audiocopy tracks of Dolby Digital and DYS if present
MP3 mixdown of Dolby Digital (128k)
"Beer is living proof that God loves us and wants us to be happy." - Benjamin Franklin 1706-1790
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