I am searching for the best GOG games in regard to their plot. Personally, I believe that the Legacy of Kain series is one of the finest examples.

So, could you mention the best plots as appear in games that are available here in GOG?

Personal favorites for their stories/general exposition :
- Outcast
- KOTOR
- Planescape Torment
- Grim Fandengo
- Sunless Sea

Also:
- Pillars of Eternity
- STAR WARS KotOR II: The Sith Lords
- The Longest Journey
- Tyranny
- The Witcher

Trails In the Sky

Trails in the Sky SC

Both have epic plots & characterization which are orders of magnitude better than pretty much any & every AAA/mainstream game ever made, except perhaps for a small handful of exceptions that are on par with them, like the Witcher games.

And after you play those two (which will take quite a while since they are huge games), you'd probably wanna play Trails in the Sky the 3rd as well, even though it's plot isn't presented in the same way as those first two games.

Seconded. Incase of the Witcher series I really recommend reading the books first since the games continue the story of the books and CDPR really put a lot of love into capturing the characters and the world - and there are a lot of references and nods which you'll only get if you know the original story.

More recommendations:

Unavowed
The Wolf Among Us
Firewatch
Event0
The Dig
Loom
Ether One

Some of my favourites are:

Anachronox
Deus Ex
Jade Empire
Loom
Shadowrun: Dragonfall
Star Wars: Knights of the Old Republic
Star Wars: Knights of the Old Republic II - The Sith Lords
Syberia
The Longest Journey
The Saboteur
Ultima V: Warriors of Destiny
Ultima VI: The False Prophet
Ultima VII: The Black Gate
Wing Commander II: Vengeance of the Kilrathi
Wing Commander III: Heart of the Tiger
Wing Commander IV: The Price of Freedom

Only if you play on the light side of the force. As a dark side character everything falls apart and it becomes painfully obvious how you have no influence whatsoever on the story (the game even admits that you have been merely a puppet on strings for the most time) and that it is actually not a very good game. The gameplay itself is pretty bad, controls and UI are clunky and consoly, especially the inventory, and combat is boring without any tactical depth despite the use of the D&D rules. The only redeeming factor in my opinion are the NPCs that can accompany the player, as some of them have quite interesting storylines. I know that many people hold this game in very high regard, and I used to be one of them, but there is not very much to it. THAT on the other hand really is a gem and deserves every praise it gets for its deep and complex story. I've played through it many times and found something new about it every time.

I second The Witcher. In my opinion, what makes the story so great is that at some point you will be forced to make difficult choices with consequences, and no option is "right" or "wrong".

I would also like to recommend Gemini Rue. I am very fond of this adventure game. The philosophy behind the story still lingers on, several months after I finished it, and the story makes you really care about the characters.

I played the light side. One of the worst gaming experiences I've had. Some of the NPCs stories seem to start promising but end up shallow. Even the good ones can't make up for what's otherwise a terrible game with terrible storytelling.

Sands of Time

As in Prince of Persia?

Good to know I am not alone. I'm trying to understand why this game is held in such a high regard by so many people and the only explanation I can think of is that they played on the light side and the story made enough sense to make them overlook the bad gameplay. Especially the "big reveal" seems to play a role, but in retrospect it is neither very original nor especially surprising.
Or maybe it is better on consoles, who knows. Or maybe there were not many good RPGs on consoles in the first place (not counting JRPGs, which are a separate thing), so console players were easier to please at that time. And most of them probably did not play it again since then and forgot about the bad parts, but just remembered the story.

Yes. I remember a nice moment spent just narrating its story to an attentive friend, as if I was summarizing a book, a movie or telling a fairy tale.

Someday I'll work up the will to do a dark playthrough, but as is I always chicken out and choose the light side :) Perhaps a little bit in part because I like using a purple/yellow/green lightsaber and those just don't look right for the dark side :P
Oh yes completely forgot about SoT, I remember being real engrossed in the story during the first playthrough. If only the actual gameplay aged a bit better (the fighting specifically). Though the story is almost, or just as good in Warrior Within, which I think aged a whole lot better. Prefer the vibe of Sands of Time though.