I would go with VirtualDubMod for AVI's. Make sure that video is set to directstreaming, then go to the streams menu and double click on the existing audio, this will disable it, then just goto add stream and add your new audio. Then just save out a new AVI.
If you use VDub for MPG, then you will have to re-encode the video and save out as an AVI, OGM or MKV. For MPG I would suggest TMPGEnc instead as you can leave the video and container as is. Use the multiplex tool to add your original audio and new mp2 audio.