There are a few gripes I've got with iTunes, all of which revolve around my subscriptions to podcasts:

1. Large downloads freeze iTunes (and sometimes the entire system) upon completion.

When a large (~250 to 500 MB) video podcast file has completed downloading, iTunes will completely freeze up. It feels to me like this hang is related to copying the file from a temporary download location to the intended destination (which is undoubtedly what iTunes is doing). Seeing as iTunes is a multi-threaded application, this should not, under any circumstance, happen. It should spawn a child thread to do the copy operation in the background, so that I can still use the application. Every once in a while, I even see my entire system hang up during this operation, which is doubly bad.

2. Some video files cannot be recycled immediately after viewing them.

After completing a video podcast, I find that I cannot immediately recycle the corresponding file from within iTunes. If I try to do so, the entry in iTunes is removed, but the file does not get removed! To recycle the file properly, I have to shut down iTunes, start it back up, and delete the entry. Somewhere a handle isn't being released properly, and the file remains locked. Again, this is a bug that could easily be solved.

3. The Windows screen saver screws up video playback.

If you have iTunes installed on a Windows system, try this experiment. Get a video file through iTunes (a video podcast for example), and start it playing. Pause the video and walk away from your computer for a while. Allow the screen saver to turn on and, when it has, come back to your computer. When the screen saver is cleared, try to play the video again. What happens? No video! This particular bug has existed for years (I've seen forum references to this bug as far back as iTunes 5 and 6), and it's apparently a known bug at Apple. That they don't get around to fixing it is very intriguing to me.