I don't know of any such program although I just record them manually. Use something like Nero Wave Editor or Creative Wavestudio to record the file. In Recording control ensure that the Stereo Mix Source or the "What you hear" source is selected and at a reasonable volume (this may require some trial and error before its perfect) Find the source where you can record the sounds which come out your speakers - it might be disguised as Wave/MP3 or some other crazy name depending on your sound card. In case of Creative Audigy 2 series cards they use the source name "What u Hear" whereas Realtek have a Stereo Mix and Mono Mix source :? Pointless as it goes without saying which is the superior source!!
Load the MPEG2 file up, set the program to record, play the MPEG2 file and then when it's finished, stop the file, trim the silent parts of the file, and save!
Sadly I'm in the same situation as you, as there are loadsa music videos from Quicktime PRO which have songs which aren't available for download for a couple of months!! so I just do it the manual way - kinda brings back memories where I had to make copies of tapes through dubbing where it would take the whole length of the tape to copy lol!