I have be using VirtualDub for years to encode video files. I found many criticisms VirtualDub is being old. We should use more modern encoder support new file format like MP4. Avidemux seems very popular as it has as GUI. No command line option to be remembered.
I used Avidemux to try to encode a few files and it seems that it could get the job done. Until recently, I found a very unforgivable feature (a.k.a. a big bad bug)! The frame detail got blurred! I thought it was a blurred by the codec at the beginning. However, when I look at the preview screen in Avidemux, the details has been destroyed already comparing with VirtualDub and Media Player Classic (which deinterlaced the frame and still looks good).
We want to minimize the quality loss of the video in many ways like increasing bitrate. Losing the quality while decoding the source file is not acceptable. Please trash it right the way!