A minor example since it's not a story-driven game, but a perfect one : in Supreme Commander the Cybrans' colors are red and black, all of their stuff is angular and most of their units look like spiders and bugs. However, they just want to free their fellow cyborgs from enslavement and be left alone in their corner of the galaxy.

Meanwhile, their UEF rivals have standard good guy colors and aesthetics, but they're the ones trying to enslave one faction and exterminate the other.

Shoot, Shrek is a lot more clear-cut of an example.

This is actually a pretty common recurring motif in the Yu-Gi-Oh! franchise, though. Half of the protagonists are associated with 'darkness' in some way or another, so it's pretty common they'll be contrasted with a rival or villain associated with 'light'.

1. In the original manga, Yami/Dark Yugi/the spirit of the Millennium Puzzle is... okay, he's not exactly a good guy at the start, but he gets better. His 'ace card' is Dark Magician, and his main rival, Seto Kaiba, is known for using 'Blue-Eyes White Dragon', which is heavily associated with light. Yugi wears dark clothes, Kaiba's most iconic outfit contrasts him with sleek silver.

Yugi's association with darkness sows the seeds for this 'dark protag, light rival/antag' dynamic being so prevalent for the rest of the franchise.

2. GX has Jaden/Judai also heavily associated with darkness, later seasons having it be an innate power he was born to control. While the final antagonist is associated with darkness, as well, the 'Light of Destruction' serves as the primary antagonist of the second season, and despite being defeated, its lingering influence serves as a catalyst for the third season's antagonist.

3. There's no getting around it. ZEXAL is about the Earth being used as the battlegrounds for a proxy war between Heaven and Hell. Despite the protagonist, Yuma, being partnered with a spirit from the Heaven-analogue, the Astral World, his own abilities later in the series ultimately reflect the setting's version of Hell, the Barian World.

While the final antagonists are from the Barian World, Yuma also does have a brief clash against the de-facto leader of Astral World in the endgame, which he wins.

This series isn't 'dark vs light'. The power of 'Chaos' that Yuma wields isn't inherently evil, but it is also used by the demonic antagonists most of the latter half of the series is about battling. But the series also makes it clear that the Astral World isn't exactly the squeaky-clean world of 'pure good' that you might expect.

4. VRAINS has a protagonist and deuteragonist artificial intelligence associated with darkness. The second season's villain, arguably responsible for most of the bad things that happen in the series, is a member of the same 'species' of artificial intelligence as the deuteragonist, but associated with light, instead.

The Godfather

Bayonetta, you're dark witch who fights holy army of angels

Star Wars

Berserk, black swordsman good/white falcon bad. To be fair the white falcon doesn't look good in his true form

Starship Troopers

The book of it - "Cabal" by Clive Barker
The film of it - "Night Breed"

Dark souls
Evil lord of sunlight Gwyn/hollow zombie dark soul bearing protagonist

Kinda surprised Berserk was only brought up once before here

Batman.

FF XIV: Shadowbringers

Don't lecture me i dont fear the darkside as you do

Fistful of Dollars

Few Dollars More

The Good The Bad and The Ugly

High Plains Drifter

Pale Rider

And everybody must remember 'Right Turn Clyde'

Outlaw Josey Wales

-should have recommended High Plains for Halloween movie its not horror but - youll need to watch it.

A different take for the Yakuza fans

"Brother"
-After a family loses a war. One of them is sent to the USA, he is considered too dangerous to be in Japan.
https://www.youtube.com/watch?v=z0a1ykPxtD4

Yes, in this film he comes across as a reasonable person imho.