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Fucking Weeaboo
nate, are you skilled enough with javascript? Because if there's a way to make it audio switching work using that, you could incorporate that with a flash file.

Outside of that or actually embedding the video and audio files separately in a flash file (or even possibly just the audio files and load the video separately, though that would probably wreck sync), that's the only ideas I have right now.
Not a walrus
Quick google search turned this up:

http://blog.gingertech.net/2011/05/01/html5-multi-track-audio-or-video/

Only problem is that I don't know how well this is supported across browsers.
Edit history:
nate: 2013-03-28 11:33:34 am
hmmmmmmmmmmm.

looks like firefox under windows 7 as of a month or two ago passes off h.264 to windows which means that going to html5 video on sda might no longer involve reencoding every video on the site.

at the very least i'd like to get away from flash asap even if playing the commentary track doesn't happen on every platform.
Not sure if I am misinterpreting what you guys are looking for but...

Couldn't you just mux in two audio tracks for the video? One with just game sound and one with commentary + game sound? You could use ffmpeg for that then use HTML5 to play the video. Since, audio track switching seems to be unsupported at the moment you could just let them download the file itself if they really want to listen to the other track.
Not a walrus
We're trying to make it so people don't have to download the files to listen to the alternate audio tracks, the files themselves are already exactly as you describe.
Edit history:
hitmanatee: 2013-03-28 02:01:45 pm
In that case you'd probably have to hack up some Javascript that always set the audio time to the video time and was trigger through events like volume changes, pause, play etc.
Final Fantasy VII Fanatic
Relevant? The Community that I've seen on SDA Is quite mature, they also host the AGDQ and SGDQ, I still see it as the number 1 community on twitch