Hi,
I know the answer maybe try CS4, I don't know how effective this would be on my current systems, but surely there must be a 3rd party out there who has resolved this issue for CS3?
Any ideas?
thanks,
Paul

Do it in After Effects.

Import a bunch of video files into AE, select them all in the project bin and drag them onto the "New Comp" icon. This will put each video into a new composition for each video. Then drag all those comps into the render queue and hit render.

Will AE render out to H.264 and/or .flv?

Yes, and with presets for ipod, apple TV etc. too.