Try "super" converter it's free, I've used it to batch convert flv files to avi with good results. And it can convert every other type of video files.
http://www.erightsoft.com/SUPER.html
But there is no one program that can do everything perfectly.
I use Winavi converter to batch convert my mpeg2's that I record from my tv tuner card to AVI because of the speed and quality. And I also use it to convert my AVI's to DVD because of the speed. This program I had to buy, but it was worth the cost.
http://www.winavi.com/en/video-converter/video-converter.htm
those are my recommendations, I use all 3 programs and found them to be reliable and fairly easy to use. Most of the times I use the default settings and don't bother with bitrates.
