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VirtualDub, you could write a batch file to initiate each encode if that's easier, or just populate VirtualDubs own batch processing list.
What do you want to do with the audio? -
Load one of the files into VDub, select the settings you want. In case you haven't already, download the Lagarith codec. Save the settings as a vcf file.
I fiddled with The VDub queue at one point but found it was easier to just point a windows batch file a directory and let it handle everything.
http://ss64.com/nt/
These are the VDub command line options http://www.virtualdub.org/blog/pivot/entry.php?id=20
My command line generally looks like this: VirtualDub /s "F:\Work\Batch\Config\Default.vcf" /p %AVSFILE% %OUTFILE% /r /x
It's possible to simply add a bunch of files to the queue using the command line but I prefer to keep the ability to mess around with the input files before they're processed. I use AVISynth for the video and process the audio separately, so you may need to adapt if you'd rather do both together. Someone may have a better idea, but Lagarith is a lossless codec, so I don't think many encoding programs support it. I'm sure there must be some. Oh, right, VDub will put them in an AVI, which doesn't handle VFR very well. If your capture is VFR I should think if you loaded the files with AVISynth using DirectShowSource and specified a constant frame rate it should add mathematically perfect duplicate frames which Largarith should simply convert into un-coded frames. You can remux them into a more modern container later if you prefer.
Hopefully someone else has a better solution. -
Assumes the Lagarith codec has been installed.
If a group of files are to have the same process applied to all.
Save a VCF/vdscript file with the settings you want then process all the files at once:
Run VirtualDub
Load one of the files.
Set the compression as required.
File > Save processing settings
Give the file a name.
Exit
Assume all the source videos are in the same folder.
Create a new target folder
Run VirtualDub
File > Load processing settings (select the vcf/vdscript file).
File > Job control
(In the Job Control window), click Edit > Process directory and select the folder containing the source videos then select the target folder.
The files to be processed should appear in the window;remove any you don't want to process.
Click 'Start'.