Biggest example would be the Brotherhood of Nod in C&C.

Grand Theft Auto V, they even got Trevor to feel like a good guy from time to time until his insane nature became a harsh reminder.

Spec Ops: The Line. but then... that's almost the point.

Saints Row of course!

Bioshock Infinite. I mean... Forget it. I won't say any more.

Dungeon Keeper perhaps? From your point of view the surface world are the "bad guys"

Mount & Blade: Warband. Because the only bad guy in this game is us! MWAHAHAHAHA!!!

All Hitman games.

Brotherhood of Nod never felt like the good guys to me, at least in the C&C games I've played (Tiberian dawn & sun).
I can't actually think of something exactly like you've described tbh. Closest thing might be Age of decadence imo. There are no truly good factions there, only different shades of grey. Some outcomes are preferable to others though. Ironically you get one of the "best" endings (one where it could actually be argued that the world might at least be getting a little bit better because of your actions) when you're playing as an assassin. You end the game basically as a secret policeman hunting down religious cultists. That might sound bad, but to me it felt satisfying and actually morally okay.

You escape a high security prison together with a few fellow prisoners and set off to pirate ships for a living -- Independence War 2: Edge of Chaos.

Baldur's Gate and Baldur's Gate 2.

And of the evil protagonist type, TIE Fighter.

Which game?

In most of the older games they acted like total douche canoes, tbh....killing people with flame tanks and such, brainwashing civilians, etc.

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As for me: If it counts the end and some cutscenes in Metro 1 make the enemy out to be a friend.....even the alternate ending suggests such.

I've never played them, but I guess the Riddick games could be called this. You play a criminal escaping from prison after all.

The Bolo Santosi/Reapers faction in Just Cause 2 felt like the goods guys in comparison to all the other factions.
Maybe it was just how Bolo spoke.....
https://youtu.be/8U-BPDDDSto

Every Star Wars game. Anyone that kills Gungans and Ewoks can only be the good guys.