The Last Federation

Not a buff yet, but I'll be getting into it.

Indie SF specifically?

The only one I've played that's on GOG is FTL and it is incredible.
GOG does have a large number of excellent SF non-indie games though.

Indie SF, but outside of gog, I can suggest/recommend:

Transistor
Hard Reset
Starbound
Kerbal Space Program

I'm not sure whether Kerbal Space Program really fits the usual SF mold, but nevertheless it is an incredible space exploration based game in which you get to build and blow up things in the most spectacular manner compared to any other video game!

Vicinity is a free first person puzzler. One of the many games inspired by Portal.
Space Quest II: Vohaul's Revenge is a free fan remake.
Dead Colony is a free Robotron-like game.

(Never played them, but thought I'd mention them anyway, since they're free!)

Drunken Robot Pornography!

And Portal. I might add a more serious answer soon.

EDIT: Woops, I missed the "indie" part!

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Sid Meier’s Alpha Centauri
My all time favourite game, and the only immersive 4X I know.
I’played it for more than ten years, and it’s still the only game I install on every machine I own.

Anachronox
An RPG by the developers of Deus Ex, with its ambiance being a mix of Douglas Adams’ H2G2 and Ridley Scott’s Blade Runner.
Funny AND dark, cynic, often suprising… A shame it is not better known!

StarTopia
Some kind of Dungeon Keeper in space (by the same developers), with the same kind of cynic humour.
Full of references ot other games and movies, a smart game easy to apprehend.

Freelancer
If you’re into dogfight in a customized spaceship, this one is still the best in this category, even after all those years.
Its arcade gameplay make it far easier to apprehend than the X series and other "simulators".
A quite long campaign followed by an open game of exploration, there is an awful lot of hours worth of fun in this one.

Warzone 2100
An open-source RTS in which you design your own units with hundreds of possibilities.
Hey, this one is free, it would be a shame to miss the opportunity to give it a try ;)

I'm not sure how "indie" Kerberos is or isn't but
Sword of the Stars is SF themed and a personal favorite, with indie feel

Then BATTLE WORLDS: KRONOS is very SF themed, though I haven't played enough of it to really comment on how enjoyable it is for a TBS game.

Strike Suit Zero is an SF space shooter and indie.

All radically different games depending on what you might be looking for. (and all here)

OT
Is the OP's avatar her picture?

If so, do guy's who own miniature donkey's turn you on? :D

Does anyone knows something about nexus sea?
https://www.youtube.com/watch?v=EBSpuEVsDtE

I was certain SF stood for SpellForce for some reason...

I either own these or have them on my to-get list. My favourites are marked with #.
Some categories overlap, like Zigfrag, which is an space shooter with RPG elements.

Rogue-likes
#Sword of the Stars: The Pit # FTL # Bionic Dues * Shattered Planet

RTS or Strategy or Tactical...some have RPG elements
* Space Pirates and Zombies # AI War Collection * Gods Will Be Watching
* The Last Federation * Space Pirates and Zombies * Deadstone
* SBX: Invasion Base Defense * Space Salvager * Star Hammer Tactics
* Unstoppable Gorg * Steam Marines * The Quantum Principle # AI Infinite
* Void of Darkness # Space - The Return Of The Pixxelfrazzer * Endless Space
* Master of Tactics * Galaxy Union * Starpoint Gemini

Space-shooters
# Ring Runner: Flight of the Sages * Really Big Sky # Photon Phighter Origins
* Solar Struggle * SOL: Exodus * The Wreckless

RPGs
# Shadowrun Returns * To the Moon
# Dark Scavenger - technically this is a sci-fi and fantasy mash-up
# Zigfrak * Greed

Platformer or Adventure or Puzzle
# Capsized * The Fall * The Swapper - this was freakin' difficult !
* Lifeless Planet * SpaceChem