Hollow Knight and Subnautica are probably 2 of my top 5 games of all times. top 5 indies would be :
Hollow Knight
Subnautica
The Outer Wilds
Return of the Obra dinn
Guacamelee 1

I really enjoyed FTL, was one of the first rogue like games i played and i absolutely loved the concept. Probably my favorite Indie game.

As for a Indie series, it would be the Ori games. They are masterpieces.

Subnautica captures deep sea exploring with fear and award very well and looks fantastic. 

Shovel Knight is just an awesome idea done right.

These games also offer amazing soundtracks, a good game is ever better with good music.

1) FTL

2) Ori Games

3) Subnautica

4) Shovel Knight

Off the top of my head, here are some indie games I've enjoyed from the past few years:

Undertale
War Groove
Broken Age
Axiom Verge
West of Loathing
Dead Cells
Untitled Goose Game
Cuphead
Streets of Rage 4

And here are some that are a bit older, but also quite fun:

Pixeljunk Monsters
Minecraft
Plants vs Zombies
Castle Crashers
Scott Pilgrim vs the World
Super Stardust HD

For me Inside, Never alone, The Witness, and Rime

Stardew Valley is the indie game I've spent the most time playing. Super relaxing and addictive, but also super well known so you've probably played it already if you like the premise.

Return of the Obra Dinn is my favourite "finite" indie game, meaning there is a story and it ends at a certain point. Super awesome and super challenging detective game where you have to relive the dying moments of the crew from a ship and determine the fate of each one. Oh, the soundtrack and animations are super satisfying and crisp (it's from the same guy as Papers, Please, so you can expect that same kind of humour too).

The Red Strings Club is pretty short and not for everyone, but I think it's the best game at dealing with robotics and ethics in the future on a cyberpunk world (certainly way better than Cyberpunk 2077). That said, the gameplay is minimal and relegated to minigames, you're just choosing things and partaking in dialogue most of the time.

Gorogoa is a beautifully animated and super relaxing experience. The bittersweet story is only told through animation and sound effects while you move squares around to form an everchanging mosaic. Super recommended.

Into the Breach is from the guys who made FTL. It's kind of a mix of strategy and puzzle. Super tough and super addictive. Also pretty cheap now, so you should get it at least to give it a try.

I forgot about Shinen.

Fast Racing Neo is a cool F-Zero meets Ikaruga mashup with some of the best graphics on both Wii U and, in its RMX form, on Switch, at a sexy 60fps.

Nano Assault Neo is a fun shmup that uses cells in the same way that Mario Galaxy used planetoids.

Art of Balance is a nice relaxing puzzle game with a nice zen-like atmosphere and simple yet elegant and satisfying gameplay.

Who remembers the granddad of indie games Elasto Mania (2000) on PC?
My favorite will always be Archibald's Adventures.

I'll throw together a quick top ten:

1. Doki Doki Literature Club!
2. Black Mesa (I think that would count, even if it's a remake of a non-indie game)
3. The Stanley Parable
4. Undertale
5. Celeste
6. Super Meat Boy
7. Hollow Knight
8. Ori and the Blind Forest
9. The Beginner's Guide
10. Braid

There are also several that I plan to play but haven't gotten around to yet, Shovel Knight and Cave Story for example.

Given Moon studios 80+ team size I don't count them but both Ori games would be at the top if people want to count them but otherwise.

1: Darkest Dungeon
2: Hades
3: Binding of Isaac Rebirth
4: Steamworld Dig 2
5: Shovel Knight
6: Slay the Spire
7: Hollow Knight
8: Helltaker
9: Duck game
10: Overcooked

Honorable mentions would be Don't starve, baba is you and among us.
I noticed that wayforward that develop the Shantae games have 155 employees so that was a bit surprising but I guess they do a lot of smaller games.

Edit: ops accidentally added slay the spire twice. But also I just love the variety of ideas that indie games have. While my list is a lot of metroidvanias, rougelikes and party games, games like Baba is you or Gorogoa truly feel like nothing I played before