Astro Boy (Tetsuwan Atom). Basically defined and kick-started anime as a genre and aesthetic. If there’s a most influential anime, it’s this.

Or maybe Space Battleship Yamato. It turned anime from “TV comics” into, well, anime.

Mazinger Z. Pioneered the giant mecha anime. Also Getter Robo.

Science Ninja Team Gatchaman (better known in the West for its adaptation as Battle of the Planets). The template for the super sentai team genre.

Mobile Suit Gundam. Revolutionised the giant mecha genre moving from simple good vs. evil children cartoons to complex geopolitical narratives. Also, in a similar vein, Macross.

Urusei Yatsura. The template for moe anime. See also Ranma ½.

Nausicaä Of The Valley Of The Wind. The foundation for Studio Ghibli’s aesthetic, tone, and narrative.

Akira, Dragon Ball, Cowboy Bebop. Brought anime to the mainstream in the West, and Dragon Ball is a cornerstone of the shounen genre, with probably only One Piece coming close in influence.

Sailor Moon. Not the first magical girl anime by a long shot, but arguably the cornerstone of the genre. Also Puella Magi Madoka Magica, which redefined and revitalised it.

Neon Genesis Evangelion, already mentioned in the OP. Extremely influential in the 90s and noughties.

Ghost in the Shell. Took over from Akira as a cornerstone of cyberpunk anime.

And I’m surely missing dozens, I’m far from an expert in the genre.

Personally Space Pirate Captain Harlock, Doctor Slump, Dragon Ball, Urusei Yatsura, and Ranma ½, and later Akira, My Neighbour Totoro, Nausicaä, Ghost in The Shell, and Fullmetal Alchemist were my main introductions to the genre (besides stuff that was in the background but I didn’t really follow or, at the time, recognise as a specific genre), but that’s just personal history and preference; I tried to list ones that seem to objectively have had significant influence on the genre or industry.

I don’t think Lucky Star and K-ON! are blueprints for CGDCT. They surely influenced the shows coming after them but any popular show in a genre does that. The consensus seems that Azumanga Daioh is the blueprint for CGDCT as before it CGDCT wasn’t a genre and after it CGDCT became a genre. For example, can we say that shows like Gochiusa that came after Lucky Star are based upon it and not on something slightly earlier like Ichigo Mashimaro, and can we say that Lucky Star is truly groundbreaking compared to Ichigo Mashimaro in its content? I would say that shows like Lucky Star and K-ON! are not genre defining but instead popularised the existing genre. If anything, that 2007-2009 era was the golden age of CGDCT, not its inception (2002) or where it finalised its form (maybe around 2005 but harder to say). So my vote is Azumanga Daioh for CGDCT.

Maybe for shows heavily leaning into Iyashikei, Yokohama Kaidashi Kikou is what really set the tone but I’m not sure. I’m going with “leaning” here because SOL, CGDCT, Yuri and Iyashikei are almost always in there together to some extend but some works lean heavier into some aspects than others.

Unfortunately I can’t think of any anime that really feel like they’re taking inspiration from Fullmetal Alchemist Brotherhood. Can you give any examples?

It feels like Sword Art Online and Rising of the Shield Hero sure got a lot of imitators though!