Wondering what I'm talking about? Me too ;).
No seriously, I wobbled back and forth for years re books and how best to store them, and here's what I'll say: I'd rather read a physical book for enjoyment's sake any day of the week. However, if I want a book to be an ongoing reference for me, I got a brand new bag: Rip-Scan-Trash. Yeah, that's about it (Of course you'll want a Tablet PC to read them on ;).
The problem for me with reference books was, I never referred to them. 9 times out of 10, I'd do a web search instead. And the books would just glare down at me from their shelf, as if to say "fine, keep your digital mistress, but we're what you SHOULD be using."
So, feeling far too guilty from the judgemental references, I recently used the Rip-Scan-Trash method to convert a number of reference books to digital. Somebody qeue the choir: using MSN Desktop search with the PDF search attachment, I CAN ACTUALLY SEARCH MY BOOKS AND USE THEM AS THE REFERENCES THEY ALWAYS WERE INTENDED TO BE. This is a big deal for me, because as Gordon Bell of the MyLifeBits project has asserted, once you physically file things, you never see them again.
And I know a lot of people like to go the route where you scan the book without destroying it for resale value: to me that's like .... can't think of anything, just wasteful timewise as ripping out the binding and ADF'ing vs. preservation is warpspeed vs. Fred Flinstone peddling with his feet. To bolster my argument to this effect, I point you to Jason Dorko's blog post on the same topic: he too concluded it's a waste of time to try and preserve the physical integrity of the book.
Underlying, I suppose.