For a while now I've been having a consistent problem with my 3rd generation iPod: the last 15-20% of some songs get cut off. Unfortunately, there seems to be nothing that Apple is doing to address the problem (or even acknowledge what it is). Several people have reported this problem in various forms. Now, I only use iTunes to import my songs, and as others mention, they play fine in iTunes. And the kicker: this is even happening with songs that I purchased from the iTunes store!
It's definitely a problem with the iPod: the progress bar gets within 15-20% of the end of the song, and all of a sudden, the iPod switches to the next song. If I manually set the progress bar into the part that gets cut off, it immediately skips to the next song without playing anything. It's not every song, but it's always the same songs. It seems like every so often a new song starts exhibiting this problem.
If Apple would address the problem, that would be great. Any hope of getting that to happen? Probably not.
My wife's 1st generation iPod mini also has a problem: In less than 3 years (it's newer than my 3rd generation iPod) the battery won't hold a charge for even 30 minutes. Is it in warranty? Not anymore! Is the battery user-serviceable? Never! Last time I checked, Apple wants $100 to swap out the battery.
By now you should know what I'm going to say: my next MP3 player selection will NOT be of the Apple variety.
Update, August 2007: I decided to go with a Zune; read the whole post