Original Quake, for most underrated! Classic Doom gets all kinds of love, and I understand it was kind of the beginning of 3d-shooters, but Quake was better imo. The atmosphere, monsters, and building design were all amazing. The skill balance was also good, managing to be difficult on Hard skill without throwing hundreds of monsters at you.
Overall I think ID Software took most of what was great about Doom, and improved on it with this one, but it doesn't get the recognition it deserves. Most people who do remember it only talk about the Multiplayer, which is a shame because Single-player is very fun and re-playable.