I keep it in the interest of archiving the whole thing. But I don't burn CDs, I just archive the FLACs. I export into iTunes friendly format, sometimes AAC, sometimes ALAC. Either way, you can go into iTunes and get info on the file. For tracks that have just audience, like maybe between the last tune and the encore, you can check the box to skip when shuffling. So if you are randomly listening to tunes, then these tracks will just get skipped. Nice.
If you choose to not to track out these gaps, you can still go into iTunes and check the box for start and stop time. So, you'll get the whole song in iTunes and any burned CDs (but I'd recommend burning elsewhere), but the song will only play in the time boundaries you establish. Again, great for cutting out the last 2 mins of a song when it really is just the encore cheering, etc.
Hope that helps. Not sure if other apps offer these capabilities. These preferences do move with the tunes to iPods so playback in the car, for instance, adheres to the same rules.
keytohwy