I much prefer a bound copy - and I do make notes in books. If I buy it, then it is something that I plan on keeping; if I do end up passing it on, then maybe the notes will come in handy for the new owner (especially if it relates to footnotes on similar topics elsewhere that were never an original part of the book).
PDF versions tend to burn my eyes out quick and Howard is definitely correct about finding points of interest and skipping the 'in between'; I find myself doing that alot with electronic copy and not something I do with bound media.
S