ASMEURER  2.0.8 works now.   
(Version 2.0.8)

ASMEURER  From email with developer:

"

Yes, but it is a little counterintuitive. You need to use "Join & Convert" and set your iTunes conversion settings to create Apple Lossless files."  
(Version 2.0.7)

3AM COFFEE SOFTWARE  Yes, that happens sometimes.

iTunesJoin uses QuickTime to join AAC files. Sometimes QuickTime simply refuses to join AAC files. Sometimes QuickTime joins the files, but iTunes refuses to recognize them. We have not figured out what causes this; you can help by sending us as much information as possible on the AAC files you are trying to join, especially how they were created. Where did you get them? Did iTunes make them? iTunesJoin? Some other program? Someplace else? (Don't worry, we won't tell.)

If you are willing to accept a slight quality loss, you can use "Join & Convert". This will join to a .mov, which, as you mention, does not work on iPod, but then uses iTunes to convert it (to AAC or MP3). Or you can set your converter to Apple Lossless; you won't suffer quality loss on the conversion, but the output file will be quite large.  
(Version 1.0.3)

3AM COFFEE SOFTWARE  We may have identified the cause of this issue. It seems to occur when joining files of different bitrates. (You can find the bitrate in iTunes' info window.)

If anyone experiences this problem, please email us and tell us whether or not you were joining files with differing bitrates.

If our guess is correct, it looks like this is a QuickTime bug. We are investigating whether workarounds are possible.  
(Version 1.0.3)

ANONYMOUS  We'd appreciate if you could email as many details as possible about the problems you are having so we can try to correct them.  
(Version 1.0.1)

ANONYMOUS  Okay, so you gave us 3 stars for features... what other features would you like to see?

You gave 3 stars for value: presumably, that's because you think there should be other features?

You gave us 3 stars for stability... what stability problems did you encounter?  
(Version 1.0.1)

ANONYMOUS  The advantage of a program like this is remove breaks between songs, perhaps ripped from a CD, where there is no pause in between. Sometimes when playing ripped tracks like that you'll get a short pause when the track changes - an app like this could remove it.  
(Version 1.0)

ANONYMOUS  AudioBooks!!  
(Version 1.0)

3AM COFFEE SOFTWARE  iTunesJoin cannot remove gaps between tracks, because it has no way of knowing how long the gaps are (and if it were off by even a fraction of a second, it won't sound right), so even if the user said, "cut off 2 seconds" or whatever, it probably would not be satisfactory. Nevertheless, we will consider adding a feature like that; who knows, maybe it will work okay.

The idea of adding various cross-fades is an interesting one. We will also consider that for a future version.  
(Version 1.0)

ANONYMOUS  I wasn't referring to blank space at the end of files - I'm talking about when there is no pause in between tracks on the CD and the gaps in between tracks appears in the player when switching between files. Sometimes if you burn those files to CD with a 0 second gap in between songs, it still has a slight tick as the track changes. If iTunesJoin puts those two tracks together with no tick in between, then I would definitely see this as a worthwhile application.  
(Version 1.0)

ANONYMOUS  Maybe if iTunes and iPod just buffered tracks properly we wouldn't need to have two versions of every CD. How long has Winamp being doing it?

In the meantime, it'd be neat if this could place bookmarks (like an audiobook) where the original tracks started. Then you can navigate it.  
(Version 1.0.2)

ANONYMOUS  this is best used for when people by a mix album. unlike some other players, the ipod has a very slight pause between tracks, so if you are listening to an album by a well known DJ, then it can be a little irritating when there is a gap between tracks. this will solve that.   
(Version 1.0.3)

ANONYMOUS  I have just downloaded a mix album from a website rather than copying from a CD. I used itunes to join the tracks back together but there is still a small skip between the tracks which is annoying. Does anyone have any tips on how to fix this?  
(Version 1.1b5)