Instapaper is really cool- save web pages for later reading in the dedicated app, which saves both full and text-only versions for offline access. I used to use iSilo with my Palm for this same purpose, but this is easier as you can save Instapaper bookmarks right on the device.
Stanza seems like a very nice (and free) eBook reader. There's a desktop app that allows you to load books onto your iPhone/iPod Touch, plus you can download Project Gutenberg books right on the device. Seems just as good as the paid alternatives...
EDIT- This doesn't come out until July 28, but seems like a much better File Magnet-
http://www.veiosoft.com/
DataCase allows you to mount your iPhone/Touch as a drive on your desktop, or FTP access as well. Browse, view, and delete files on the handheld. Seven bucks, I'm glad I discovered this before paying for File Magnet...
Thanks much for the heads up on DataCase. I was really intrigued by File Magnet, until I realized that you must have Leopard (I only have Tiger). Now I can get even more functionality that will work with my iBook. Any idea on how much it'll cost?