You can do this with either VirtualDub, AviDemux (doesn't need extra codecs) or Xmedia Recode.
First, you gotta rip the audio out of the one file, preferably with GoldWave 4, because then you can store is as WAV, which is uncompressed, you need that to sync it.
Second, make sure your audio is EXACTLY the same lenght as the video, we're talking thousands of seconds here. A difference of e.g. 0.234 seconds is okay, more than a second prolly will be bad.
Third, IF they are the same, open the video with either Vdub or AviDemux and look for the Add Audio from different source option. Add the WAV file. If it's sync, you can then use compression to make the movie smaller.
You can adjust the length of the WAV file in Goldwave. You can do this, even when they are completely different and have totally different starts and endings. But that's hard.
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Couldn't locate decompressor for format 'XVID' (unknown) VirtualDub requires a Video for Windows (VFW) compatible codec to decompress video. DirectShow codecs, such as those used by Windows Media Player, are not suitable.
Looks like VirtualDub supports only one format... – Rookie – 2012-04-06T12:42:02.6031
@Rookie No, it supports pretty much any format, you just have to install it correctly with XviD support.
– slhck – 2012-04-06T13:21:20.467