Syberia was good, but it ended in a pseudo-cliffhanger that was resolved very poorly by Syberia 2.
I mean, Arctic Penguins?
As far as the best goes, Planescape: Torment
Honorable Mention:
-Baldur's Gate (The sequel had the better gameplay and villain, but the first one had the better story)
-KOTOR 2 (It didn't play as entertaining as KOTOR 1, and it's ending seriously detracts from the experience as a whole, but purely as storytelling this is 4/5ths of a great game. A war-torn galaxy, opportunistic cartels and bounty hunters, a planet trying to rebuild, a former bounty-hunter trying to restore his race to greatness, the Battle of Iziz, a former Jedi trying to re-find his connection to the Force to save the remnants of his dying order being trained by the master of the one who brought the Republic low...)
-Mafia
-Deus Ex (if the game consisted only of its first half it might be tops, but the story degenerated into a lab and army base shooter for the second half, except for the grand finale).
-The Longest Journey (another game with a great first half. I don't even mind the surprise letdown at the end, but I thought the second half with the mermen and winged people was too "raw adventure game" relative to an otherwise extremely complex, detailed, colorful story.
-Quest fror Glory 2: Trial By Fire (sure it ripped off most of its plot from Arabian Nights, and by today's standards it's far too short and "empty"--it could probably be completed in two hours--but those are a magnificent two hours...the gempiece of one of the great series in early gaming)
-FFVI (this perhaps doesn't have the depth of detail that more modern games can afford to dive into, but the framework for its story is one of the best around)