Wow. I didn't realize this was such a big problem. In the past I've had a handful of songs disappear, I didn't think much of it. Lately though I've been coming across a bunch. Before downloading some new music I thought I check google and see if anyone else had the same issue. I see now that MANY people do and I gather from this thread that Apple doesn't have a solution. I thought I would add my name to the list for whatever it's worth.
In my case, there are 2 scenarios, in one the song/album is listed, but when I try to play it, iTunes tells me it can't be located. In the other, the music doesn't show up in iTunes at all. As best I can tell, this 2nd scenario only affects the albums I've purchased from Amazon in the last year or so. In both cases, the music is no longer in my laptop. I've got (or should say, I HAD) over 85 GB of music and 55 GB of audiobooks. I haven't checked them all, but as best I can tell my audiobooks are not affected. They all appear intact.
I'm not getting rid of my iPods, I like them too much and use one every day, but I am going to check for another program I can use to transfer my music. Even if everything is backed up, it doesn't really matter. Managing your music library shouldn't require constant maintenance and verification, especially after all the time that's been spent building up that library over the years. Deleting items from my computer is a dealbreaker.