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Artifact Title: Quake referred to the protagonist in the game's early stages, then to "the enemy" in the supposed final game. In the end, neither the first game (or any game of the series, for that matter) makes reference to any thing in particular.
Follow the Leader: Quake, with the antecedent of Doom, began the multiplayer experience in the 3D FPS genre, but Quake III: Arena, along with its rival game Unreal Tournament, paved the way for the multiplayer FPS. 10 years later, it's still one of the biggest feuds in the gaming history.
In Name Only: Aside from II, IV and Enemy Territory, none of the games' "plots" have anything to do with each other. Indeed, ID originally wanted the "Strogg" arc to be an entirely new franchise, but ultimately decided the game needed the brand recognition which the "Quake" name would bring. (Also, their original idea for a franchise name was already trademarked by someone else.) Quake III Arena's story makes an attempt to unite the different Id universes until that time into a single story arc.
Killer App: People built new gaming computers to fully experience the first three games, but the most notable instance is GLQuake, which caused the 3dfx Voodoo Graphics accelerator card to become a must-own for every gaming computer at a time when software rendering and 320x240 resolution was the norm.
Speedruns of the first two games will show you how high a player can rocket or grenade jump, given the right equipment. Even some secrets in Quake required doing a grenade jump. It's lampshaded in one of the secrets of the second game which requires you to do this:
Secret Area. You crazy rocket jumpers!
In the Quake II expansion pack The Reckoning there's an area with an Invulnerability item which will vanish when you come closer, of course, by rocket jumping:
No reward for you, jumper!
Many maps in Quake III: Arena and Live are designed to reward skilled users of the technique. In the latter, there's even a tutorial!
Even in Quake 1, it was useful. In the two last levels before the boss of the first episode, rocket jumping could skip half of the level, and even lead to a quad damage item.
Self Plagiarism: The first game was pratically identical to Doom in gameplay and theme, with the only major difference being that it used true 3D instead of sprites. Quake II and III subverted this, the former by having a different theme, the later by focusing solely on the multiplayer aspect.
Shout-Out: The boxes of nailgun ammo have the Nine Inch Nails logo on them (which makes sense, since Trent Reznor composed the music for the game.)
Slash Command: One of the earliest series examples, if not the earliest.