Another vote for VirtualDub.
Also, sometimes you need to handle the audio file portion of a conversion separately. For example, I have had .avi files I wanted to convert to MPEG, but ran in to cases where the video portion of the clip was in Divx, the audio in MPEG 3, this is very common, and most converter programs will not work. With VirtualDub I the load the clip and extract an uncompressed .wav file from the clip's audio portion, then open up Xing Encoder and compress the video portion of the clip together with the .wav file I created, resulting in an MPEG-1 clip. Works sweet.