I took a quick screenshot from both PC and PS1 with "best" emulations settings.

The difference is really not big, and the positives from running the PS1 version an not be overlooked.

With that said, GOG and some modders really did magic with the PC version. Kudos to them! :-)

I notice 2 or 3, maybe 4 differences

1. The map on PS1 is different for obvious reasons (TV vs monitor)
2. The smoke seems more dense on PC (but that's probably due to timing, not graphics - in the second screenshot Snake has let that smoke out a good while ago, while on PC it's fresh)
3. The shadow looks denser on PS, i think?
4. The texture quality for Snake seems better on PS, i think?

But the PS screenshot is of higher resolution for some reason

The emulator runs at 1920x1080, the first screenshot of the PC-version "only" at 1280x1024.

Here's a 1440x1080 picture of the PC-version.

So overall, do you prefer the PC or Ps version?

The PS1 version is more ”complete”, so that’s probably my go-to version, but the PC version is no slouch either. The GOG and fan fixes really lifts it.

They look exactly the same...

PS1 emulation on BeetleHW with all the bells and whistles, this is my preferred way to play.
It's not flawless, codec text glitches and some cutscene video weirdness, i haven't played the entire game on this emulator yet but so far it's fine.

The codec text glitches can be fixed using Vulkan I believe, I get the cutscene video weirdness, some portions of faces become incredibly pixelated and glitched out, another issue I have is water and stealth effects cause extreme framerate drops and choppiness. Being underwater in the beginning and when Grey Fox showed up after the Ocelot fight, it gets annoying but other than that I agree, the PS1 version seems to be the way to go but I'm hoping the PC version receives fixes and updates to put it on par with the PS1 version.