The rumored larger iPad, if it ever sees the light of day, would probably be aimed at this kind of use.
Something about associating a piece of information with a physical location on a real object makes everything "snap" together better in my head ("Oh, I remember this concept, it was about a third of the way through Dummit & Foote. Yep, it's all coming back now.").
I can still pick up my calculus textbook from a class I took 5 years ago and open more or less in the right section of what I'm looking for. I've associated that object, it's weight, feel, and size, with the information it contains.
I can't say the same about any of the dozens of pdf's I have on my tablet. I'd probably have trouble opening the right file, let alone where inside that file the information is!
If it matters or is long-term knowledge, I always get the book. (Even if given the insane pricing of textbooks, I wish this didn't have to be the case...)
If it's going to be a constant reference, I would prefer a searchable ebook as it is a lot easier to carry many of them on my Nook too and from work.
If it is a book I am reading to increase my knowledge of a subject but not one I expect to be a constant reference back too, like a study guide or the like, I prefer a print book.
Then again, I'm not sure what UI modern eBook readers have for setting and going to bookmarks.