Sundered: eldritch edition

Played a lot of these in the last two years, with Ender Magnolia and Nine Sols being my favorites among them.

All-time I think I'd still go with Super Metroid, despite its age and having completed multiple playthroughs I still end up playing for hours anytime I boot it.

Honorable mentions for Rabi-Ribi (don't let the cutesy anime artstyle fool you, this is a fantastic non-linear game with some of the best boss battles in the genre), the recent Momodora games and the Team Ladybug games (with Touhou Luna Nights being my favorite of the three).

Castlevania: Aria of Sorrow

I haven't played very many, and these might not be pure Metroidvanias, but I recommend:

The Messenger

Pseudoregalia

Tunic

Rogue Legacy 2, if it counts. Otherwise, Axiom Verge.

Supraland

It's a little old and more Metroid- than -vania: A Robot Named Fight

EDIT: since no one else mentioned it, Timespinner is kinda good too, despite being a somewhat short game

I haven't seen Shadow Complex on here yet.

It's an older title (2009) and even the remastered version is from 2016.

Still one of my favorite Metroidvania type games.

https://store.steampowered.com/app/385560/Shadow_Complex_Remastered/

I was shocked to see no mention of Ori in any of the comments here before I realized you had already recommended it in the OP. I have no issues with seconding that, the Ori series is really good.

A bunch of good ones have already been mentioned (SOTN, Nine Sols, Super Metroid), so I'll just mention some that were missed.

Castlevania: Dawn of Sorrow (sequel to SOTN, just as good if you can get past the DS touchscreen BS. The new remaster might get rid of it)

Bloodstained: Ritual of the Night (made by Iga, creator of Castlevania: SOTN, Dawn of Sorrow, and others)

Salt and Sanctuary

The Messenger

Metroid Prime. It's the only series I know of that is fully in the genre and is also not a 2D platformer.

It's insane to me how many Souls Likes could be 3D Metroidvanias if they used special powers to clear obstacles instead of just keys or random triggers to unlock new areas. That's really the only thing I see that separates the genres.

Sekiro is closer than any other, but it's mainly just 1 thing you don't have in the prologue (the grappling hook). I would love a game that is 3D over a 2D platformer, but also has the unlockable traversal tools the way Metroid or Syphony of the Night had.

La mulana 1 and 2, animal well for puzzles.

Metroid dread, highly recommend for combat.

Dead cells and rouge legacy two for rouge lite bits

terraria for minecraft + metroidvania

time spinner, bloodsworn for more typical metroidvania

the old castlevania games are on steam, so there is that

almost metroidvania suggestion is Outer wilds. Progression based learning. just not in a 2d plane and no fighting.

Super Metroid will always be my favourite. I also enjoyed Axiom Verge and Bloodstained ROTN.

I generally like shorter Metroidvania like Iconoclasts and some of the Shantae series or even Yoku's Island Express which has some backtracking.

The Metroidvania tag is a bit like Dubstep in music, a lot of those Dubstep tracks aren't Dubstep but they can still be fun for some people.

Just so it's not forgotten to time I want to recommend AM2R (Another Metroid 2 Remake). It's basically what if Metroid 2 was made in the Super Metroid engine.

I'd recommend any of the 2D Metroids, but if you're going to play Metroid 2, that's the version to play.

Batman: Arkham Asylum. It doesn't come up a lot, because only that first game is a metroidvania and Arkham City might be most people's favorite in the series, but it absolutely counts. I love Arkham combat. It's better in the sequels due to some slight tweaks in game feel, but that combat in a metroidvania is just excellent, and the game is just so well paced. It's a shame what WB did to that studio.

I don't know if it's "favorite", but an old classic was Aquaria. It had a surprising amount of content, even to the point of several secret bosses, and an absolutely excellent soundtrack. Sadly, the main guy behind it is dead now. Ori was also fantastic.

I really like Rabi-ribi

Ghost Song is one of my favorites that doesn't look like its been mentioned yet.

Aria of Sorrow

So many solid suggestions here already. I have a soft spot for the more retro styled games, and despite being short Gato Roboto is one of my favourites. It just feels so good to play.

Record of Lodoss War: Deedlit in Wonder Labyrinth is a fantastic experience.

I haven't seen it mentioned and granted I've not played it but I've watched both be played and Blasphemy 1 and 2 seems really, really good.