"Reputation is our system for measuring how a player behaves in game," Hammock writes. "We want to provide a means by which a player can judge the aggressiveness of other players at a glance." Pathfinder's rep "has no bearing on your interactions with NPCs, quests, escalation cycles, or other PvE content."
Alignment features two components. One, the player's core alignment, is chosen at creation and "is the intended alignment of the character." Active alignment, on the other hand, "begins at core alignment values but changes based on player action." Specific examples and much more detail are available via the links below.