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I am planning to make a video with commentary. I have two programs I want to record as SEPARATE tracks [one's Skype for a second person's commentary, and the other is the program I'm commenting on], while recording my commentary from my computer's microphone as well. All three audio sources are to be recorded simultaneously.

Do you know of any programs that can record audio on an application-by-application basis like this? Or, is there a way to do it in Windows itself?

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Try this: http://wiki.audacityteam.org/wiki/Multichannel_Recording

Audacity should do the trick, just take a look at the link I've posted so that you can be well informed.

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