The best part of the anime was just season 1 (all of Duelist Kingdom and then stopping at one battle after they get back). The anime never followed the rules of the actual game, which is pretty funny
(oh, summon Blue Eyes, summon him again, and again, MERGE FOR THE 3 HEADED MONSTER FOOO~)
But the Manga is a lot better. 4Kids (or whoever did the anime) took out a lot of stuff, which is reasonable since it was a Saturday Morning cartoon, but there was actual blood in the manga and people's lives were actually at stake. The game of Duel Monsters was really a dark arts game that the Egyptians used to play and peoples' souls actually got took when they lost and pretty much went to hell
It wasn't all that "light" really.
One thing that I can recall (because I actually watched the anime all the way through for the first season) is that the anime tries to portray Pegasus as this "not really bad guy" because he's hosting this tournament to try and revive his long lost love, but really he's just trying to steal the technology to see his lover from the dead. Not as bad in comparison, not so quite "Disney".
During the semi-finals Joey and Yugi never battle, Pegasus cancels and tells them they both will win their prizes and he ends up dueling Yugi for the release of his Grandfather's (and Kaiba and Bro's) souls.
The other instance that stands out is when he actually looses the game with Yugi. When he looses with Yugi in the anime, his Millennium Eye gets "taken away" and he's just left in the chair unconscious and his body guards take him away (later to get a replacement eye). In the Manga, his Millennium Eye still gets taken away, and when they show his face there is blood just all over leaking out of his socket and he's dead. His body guards then take his DEAD body up the stairs and away. (but he goes to heaven to see his lover anyway).
Though I still say it's 'fun' to watch the anime despite it's corny voice acting (I have Season 1 on the comp
) and the Manga is cool, too, just because there is a whole arc before the actual card game (and putting together the Millennium Puzzle) where they play other Dark Games besides Yu-Gi-Oh. I remember a cool section where they were playing Bakura (will they ever learn he's bad?
) and it was pretty much a game of Dungeons and Dragons but they were the pieces in this actual kingdom (shadow game) it was pretty cool.
I also read the end during the "Egyptian Arc" where they spend their time freeing Yami Yugi, and that was pretty cool as well because it was different, old, Pyramid puzzles.
So Pretty much I read from the beginning all the way up to the end of Duelist Kingdom and then skip to the end
(or what I think is the end).