Most of my audiobooks are borrowed from the library. I use the iPod Touch Overdrive app to listen to them, (awesome app for audiobooks!) then delete them as soon as I am done with them. The WAV files get transfered to my iPods (mostly the nano) as well, then removed. I try to avoid those, since the audio quality is horrible and the transfer too much of a hassle.
I have a few audible books as well, since I got them for a special price along with my kindle books, and use the audible app for them.
In order to track what I listened to, I add them all to my Goodreads book lists.