Gears: cover shooter

Prince of Persia: realistic animations with weight. also popularized a platformer subgenre, which was called cinematic platformer but unfortunately the life of the subgenre was cut short due to the advent of 3d.

Diablo: ARPG genre, and even more so loot rarity system (especially the four tiers common/rare/epic/legendary) and affixes in loot as well.

Half-Life: a lot of good things, sure, as pointed out by other comments, but I will also never forgive valve for popularizing the game not fucking starting for ages.

Rogue and maybe more so Nethack: roguelike mechanics.

some really obvious ones are Tetris: falling block puzzles and Sokoban: pushing block puzzles.

also now pretty much obsolete but Overwatch: loot boxes. they existed before, but Overwatch made them an industry standard.

Crush the Castle inspired Angry Birds and several other games with the same catapult mechanic. Loved that flash game way before Angry Birds was put on the App Store.

Arma 2-3 have been responsible for at least 3 major multiplayer genres.

Street Fighter 2 popularized and pretty much set to stone what a tournament fighter game should be. Mortal Kombat came first, but its single-player progression was this weird "tower" with some gimmick fights thrown in, like you vs 2.

Thinking about it, I'd say Mortal Kombat popularized the "REALLY fucking cheap sub boss/final boss" that many other fighting games have (looking at you, SNK) - I mean, good luck getting close to Goro in the first place.

I wonder which korean mmo could be considered as the one that de facto popularized pay-to-win as an integral mechanic.

Diablo hands down popularized not only the action RPG genre, but also having enemies as loot mystery boxes. One lucky kill and you could get your hands on a really great piece of equipment. The amount of clones speaks for itself.

I think Gran Turismo popularized the "carreer mode" of racing games.

WASD + mouse aim in FPS. Wolf3d, Doom1 and Blakestone used the arrow keys, spacebar and Ctrl back in the day. The arrows were turn, not strafe too.

I reckon it was some friends of mine in the 90s in Box Hill, Melbourne, Victoria who were the first to use WASD/mouse aim. Share house above a shop at the end of a tram line.

Ocarina of Time is the mother of modern 3D gaming with Z-targeting.

I'm not 100% sure if factorio was the first, but the devs at Wube certainly perfected the idea and now there's a whole market for the "factory game" genre.

Skyrim for the horse armor dlc.

Don’t know if this counts, but Resident Evil 4 killed off the tank controls and single-handedly popularised third person cameras for survival horror games.