Depends entirely on the PDF and how much use I think I'll get out of it. Like most of my gaming materials, PDF's get a work-out in the preplanning rather than the actual game. By and large, a lot of information tends to get cut-n-pasted into adventure notes if I think it's going to be relevant, or printed and stored in a binder if it's going to be pertinent to one of the players. I don't like looking through a dozen books to find one peice of information in the middle of a game, regardless of whether they're electronic or not
(Incidently, that's one of the reasons why I've started cutting and pasting relevant rules such as weather conditions and the effects of extreme temperature into an appendix for some of the more recent CGW products - if the pagecount isn't a big deal for a PDF, why not have the information handy so people don't have to go searching for the rulebooks to crosscheck stuff).
That being said, there are about a half-dozen full PDF's in a folder on my game desk (the malhavoc psychic stuff, Enpub's Everybody Else and Liber Equitas I and II, as well as the full version of Tornaments Fairs and Taverns) and at least half a dozen PDF's that get their own folders or are spiral bound - Cry havoc is the only real d20 product there, but there's a bunch of mini-systems like Motocaust and Cat among them.