Beyond the presence and the permanence, there's also an interactivity that I love -- and that no eReader can even come close to.

I usually take a highlighter and a pen to most books these days. Interesting passages get marked up; the margins are perfect for capturing the related thought, realization of a tie-in to another book, and whatever else; and the growing forest of dog-ears helps me find my way back to harvest all the notes later.

(I'm actually really bad at going back and harvesting the notes into a useful digital format -- but I guess the presence of all of them on my bookshelf gives a nice safety blanket, you know? They're there, waiting for me.)