The most irritating ones are where the last track has ten minutes of silence separating the "bonus track" - sometimes I'm not aware of this until it's on the player and it goes quiet. I'll either edit the WAV, or set Grip's start and end sectors when ripping, depending on whether CD drive time or my personal time is the highest priority to me.

I've never seen a disc with a bunch of empty tracks between the last real track, but I think it'd be less of a pain.

As to how I arrange them in playlists, it depends. Some obviously need the separation, and I have a 10-second silent track I use for that (in some cases, multiple instances, but never more than 1 minute). Others could easily have been part of the original album, and just go in at the end.

Some CDs have bonus tracks that weren't on the album when it was originally released on vinyl. In some cases, these are singles or B-sides, and they go loose in the artist's playlist. In other cases, they are outtakes or previously unreleased tracks - I often put these into a sub-playlist, so I can select the original album (tunes icon), the bonus tracks ("bonus tracks" playlist) or the whole lot (play icon). Often, I set track numbers to 0 if I think the bonus tracks are thrown in and the order doesn't matter.

In one particular case (Capercaillie's "The Blood Is Strong" re-issue), there are 6 bonus tracks: 3 from each of two TV series' soundtracks. I consider these to be two very small bonus albums, and have playlisted it as such.

I do agree with you that in general, "hidden" bonus tracks are a pain - why can't the labels just make accurate labels (on-disc and on the inlay) for their CDs?