Personally, I'll have to go with The Commoner Handbook. It's nice to learn how to optimize your favorite character archetypes and classes, but there's something to be said for being able to make the worst class in the game competitive. The Commoner Handbook is actually what inspired my idea for a commoner-only E6 campaign, though I have yet to be able to unleash that monstrosity on anyone yet. Most likely, though, the Handbook will be required reading for that game, if only to give everyone an even footing.
"If you find yourself falling into madness, dive." -Malkavian proverb
I love summoning so the summoners handbook is a natural choice for me. I can appreciate the effort and research that went into treantmonks wizard guide and I recognize he has his facts straight, but his tone just sticks in my craw, I just don't like the /way/ he writes. Even if his handbook is still my go-to-guide for wizard knowledge
AnarchsCry, I would play a Commoner game with you.
My favorite handbook is probably the one on the old D&D 3.5 wiki as the "Dungeonomicon." Technically a sourcebook rather than a handbook, if one made entirely by fans, the Dungeonomicon has a huge list of information in it- ranging from random discussions of biodiversity among the top predators to the weirdness of the economy.
I think the reason I like it so much, though, boils down to the fact that it has settled in my mind when D&D and Pathfinder "really" take place- in the Iron Age, when small tribes and rising empires all battered each other into submission, the wilderness was really wild, and if five people take over huge areas of land there isn't much geopolitical hubbub about it.