Here are some that come to mind in roughly chronological order:
Adventure - This action/adventure game was popular on the Atari 2600 during an era where people mostly bought the system for console ports. So many design basics in both action/adventure and action/rpg games can be traced back to Adventure.
Tempest - An intense 3D action game from the year 1981...way ahead of it's time.
Ultima 3 - Not the best in the Ultima series, and yet most JRPG's can trace their game mechanics back to this.
Ultima 4 - Arguably is the best in the Ultima series and is so ahead of it's time that no one has tried to copy or improve on it since.
The Legend of Zelda (NES) - The #1 reason the arcades died. This type of game would neither work in arcades nor on the computers of the time. You had to get a console to get this kind of experience.
Metroid - A platformer that scrolls both vertically and horizontally. Also another game that where you needed a console to get this kind of experience.
Mike Tyson's Punch Out!! - Dark Souls combat is highly inspired by this game. It was also probably the best looking game on the NES.
Super Mario Bros 3 - I italicized this, because this is probably the most impressive game on this list. Keep in mind that the killer app that launched the Famicom was Donkey Kong (arcade port). Super Mario Bros 1 became the NES's top killer app, because it was leaps and bounds ahead of Donkey Kong. It introduced side scrolling, music and a lot of other staples in gaming that many other NES games copied. And yet Super Mario Bros 3 is just so far beyond Super Mario Bros 1. All of this gaming evolution happened on the same console. It's just so amazing to see gaming progress from Donkey Kong to SMB 3 and yet both were killer apps on the same console.
Civilization - It invented 4X games and really popularized strategy games in general. I still meet young people today that love playing Civilization and yet the current games are just elaborations on the same basic formula. The best part of this game is still some similar experience to where you develop tanks and then roll over some other civilization with warriors or a phalanx. A timeless, classic design.
The Secret of Monkey Island - The character design and world building is still better than most modern games.
Final Fantasy 4 - This is the first video game I played where I actually cared about the story. It was done so well, that the story is still more engaging than 99% of other video games.
Shining Force - Every good tactical game that has followed owes a lot to Shining Force.
Dungeon Keeper (1 & 2) - These games basically invented the Tower Defense genre many years before anyone knew this genre existed.
Ultima Online - Made MMO's a thing before anyone thought this type of game had a market.
Grand Theft Auto 3 - I've never actually played this game, but I've played a lot of 3D open world action games that would never exist if it hadn't been for GTA3.
World of Warcraft - There are two types of MMO's. Those made before WoW and those made after. The two types are very noticeably different.
Wii Sports - Motion Controls are a permanent part of gaming and it started here.
Minecraft - This game now fulfills the role that Legos used to play in the lives of young children.