I agree the hidden tracks are a pain.

I haven't seen an easy way to deal with them. I wish that the hidden track info could be somehow encoded into the CDDB data and then rippers could read that information and behave accordingly.

I have done all of the following things in the past:

- Ignored the issue and just let the two track get ripped as one long track with a space of silence in the middle. Often I just hit the skip button when the silence starts playing.

- Adjusted the "ending time" of the last track in the ripping software to grab the last "regular" track, and then adjusted the start and ending time of the last track to grab the hidden track.

- Split the MP3 into three songs (lastrack, silence, bonustrack) using the splitting utility in GapKiller, then discarding the middle one (silence) and VBR-fixing and retagging the remaining two tracks.

I've never gone to the trouble of cutting up a raw WAV of the track, too much of a pain dealing with huge files in CoolEdit.