I made a database where I can look at views containing, classes, races, monster, npcs, spells, feats, items and such. Or I can read the entries in the order they were in the book each book. The great things about the views is that no matter what spell from what book if I go the the spell by alphabetical view, it's going to be there and I don't have to go looking through sources. I can either look at said views by setting or all settings together. I have settings broken down to FR, Greyhawk, Lone Wolf, Conan, EverQuest, etc.
I also use scanned pdf copies of books I own and run them through an OCR so I can put books I didn't get on PDF into the same database.
It took a while to get the major database design down, and I have to tweek it every now and then when some new type of element is added, not to mention the whole OCR thing can be a pain, but it sure beats looking through the 250+ D20/D20 based OGL books I own. Not to mention every d20 dragon magazine (274 on).
Oh, and the full text searching is the bomb too. Say I wanted to design a whole set of adventures around drow. Well, I can go to my monster view and do a search on drow and any monster with drow somewhere in the description is all that's left. Leaves me with stuff like deep gnomes, drow, driders, chitine, deep dragons, black unicorns, all kinds of nice stuff that fit the drow theme.