I'm doing a series on what I think are the best comic story arcs I've read. You may not agree, and that's the point. It's my opinion, not yours.
1. The Dark Knight Returns: This is the entire reason why comic books started to not be only for kids and why guys my age can read comics and still be looked at as (mostly) normal. Batman was already a dark character, but Frank Miller kind of turned that up to 11 with this seminal miniseries. It starts with Bruce Wayne as an old man taking up the cowl once again to fight a crime situation that was worse than it was when he was in his prime. It ends with a showdown between two of the most legendary icons in comic book, no, recent human history. The whole thing is just raw badass.
2. X-Men - Dark Phoenix Saga: Holy shit. Words can't even begin to describe how seminal this was. For me, the whole concept that a human being (of course, a mutant) could possess such godlike powers was one of the things that made this story arc so good. It just brought the Marvel Universe together for an event unlike any other (at the time) as everyone fought either for control of Jean Grey or just to keep her out of the wrong hands. Too bad it didn't get proper film treatment...
3. X-Men - Days of Future Past: Before the Terminator and his follow-up movies portrayed a dystopian future in which machines rule and humanity is reduced to a ratlike state of resistance, X-Men did. That's right, folks, this story arc which portrayed a grim alternate future came a full three years before James Cameron's sci fi classic.
4. Ultimate Spider-Man - The Clones Saga: Ultimate Spider-Man is just one of the best series of this generation. If you haven't read it yet, please do. The entire series (which I'm still reading) has had me hooked ever since I started. Brian Bendis is just that good. The Clones Saga, in which Peter Parker encounters clones of him with different features (including a female clone), deserves special attention. It just had so many "holy shit!" moments, including one involving Dr. Octopus. At that point, everything in the series, especially Peter Parker keeping the fact that he was Spider-Man under wraps, just came full circle. Damn.
5. The Punisher: The Slavers: Comics have become increasingly dark throughout time starting with the title that was #1 on this list. Garth Ennis' run on the Punisher series with Marvel's MAX imprint is probably my favorite series of all time because it's so dark and so realistic. In my opinion, it takes comics to a level of realism and darkness that most writers refuse to go to. The individual arcs all deal with dark subjects that are grounded in reality ranging from corporate crime to mob wars to Soviet military officers who think their war isn't over. This arc has to take the cake. It's over human trafficking. Human trafficking. And it revels in it and tackles it, a subject that no one else in the medium before Garth Ennis (that I know of) ever even dared to touch. Very bold. One of the reasons why Frank Castle is one of my favorite characters is because he deals with the people in this world that really deserve to be dealt with. And he doesn't subject them to some sorry-ass lame justice system. He kills them in the most horrific, nasty ways possible. Do evil unto evil. That concept is very evident in The Slavers.