Step 1. Install ffmpeg.

I believe I downloaded it from here

There was issue with the installation. After installing it (in c:\windows I believe), I noticed that none of the presets worked. This is natively a linux app, and after a bit of poking around I saw that it was looking for the presets in /usr/local/share/ffmpeg.

To fix this, I created that folder in the root of the disk I was using for the transcoding (X in my case), and put the preset files in there. After that, it worked like a charm.

Step 2. The handy dandy ffmpeg command with some batch wizardry:

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for /f %G IN ('dir /b raw\*.AVI') do ffmpeg -i raw\%G -b 2000k -s 640x480 %~nG.flv

Enjoy.

Update

The windows Imagemagick packages has a ffmpeg binary bundled in. As a bonus, it appears to work better in my limited testing. Download it here

Update 2

To rotate 90 degrees.

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for /f %G IN ('dir /b raw\*.AVI') do ffmpeg -i raw\%G -b 2000k -s 640x480 -vf "transpose=1" %~nG.flv