Soul Hackers & Rocket Knight

While it's not The Legend of Zelda on the nes, that is one of my most played games something I'll play through once per year.

Agree with some other picks here with Yoshi's Island, Banjo-Kazooie, Mega Man X and Arkham Asylum.

I'd say Digimon World. It was a very special game even though it had some technical issues and they never really managed to hit the same charm of with the sequels.

Completely forgot about this one for some reason. Guess I thought of it as a continuation of the original. Which it is in a way, but totally its own franchise.

If we cheat a bit and include sub-series's, then Metroid Prime 1 is the greatest Prime game, and one of the greatest games ever made, due to its incredible world design, atmosphere, and immersion.

Sub series should count why I said Soul Hackers as that game has a dedicated Sequel. Tho Soul Hackers is not the second SMT game.  If someone made a thread best 4th or 5th game and said Persona it would count even tho it's part of the SMT series.

Possibly a hot take, but Starfox.

While Starfox 64 benefitted from superior technology and performance, I feel like the SNES original captured the feeling of an epic space opera just that little bit better; the settings were more interesting (Macbeth as a volcanic hellscape was cooler than it being a factory planet, Fortuna as a dinosaur planet was cooler than it being a snowball) characters actually died instead of just going back for repairs which raised the stakes, and the soundtrack hit harder.

Dark Souls. The later games would improve on the gameplay, but the setting, atmosphere, and lore is the strongest in the first one.

Valkyria Chronicles. Again, the games that followed, especially Valkyria Chronicles 4, made improvements and added more variety to the gameplay, but the story and characters are the strongest in the original.

Grandia. The second game is very good too, but the first is still the best one. Great battle system, story, music, and characters that still hold up.

Metroid Prime
Dark Souls
Starfox
Half-Life
Xenogears (for the whole Xeno series)

Plenty of 2 titles franchises like Subnautica, Talos Principle...

I haven’t played that many full series, and I think I will limit it to franchises with at least three games. The easiest one that comes to mind for me is Gears of War. It’s a really consistent series, but I think the original feels more special and tight.
I have only played a little bit of Bioshock 2, but I would be surprised if it would exceed the original. Bioshock Infinite was a major disappointment imo.
The original Doom is for me still absolute perfection, and while the series has many good games, nothing beats the original.
I imagine Banjo-Kazooie would also fit, but I didn’t play Nuts and Bolts.
I also only played a little bit of Resistance 3, I doubt it would top the first one. The second game is trash imo.

Some other popular choices like Halo and Batman Arkham Asylum I feel just got edged out by their sequels.