My usual is:
ffmpeg -i input.wmv -s 320x240 -ar 44100 -r 12 -b 400000 target.flv
Where 320x240 are the dimensions, adjust at will... 12 is the framerate, depending on the site/application I'll go higher like 16-20... And 400000 is the bitrate (400 kbps). 44100 is the audio sampling frequency, and I don't add it for any reason other than I read on some blog that I should.
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