Hard to argue against Dark Phoenix saga, and if I had to pick a mini-arc it would probably be "Days of Future Past." That team was just on fire. Miller's original Daredevil run still holds up (I'm loath to pick mini-series such as Dark Knight and Kingdom Come because I feel like this thread is more about arcs that existed within ongoing continuity). Oh, and Daredevil's "Born Again" arc too, for sure.
Denny O'Neil and Neal Adams' Green Lantern/Green Arrow run deserves a shout out for having some amazing stories but also for moving the bar forward in terms of what kind of story content could be attempted within the Comics Code; I don't think you get Claremont/Byrne's work on X-Men without it.
We gotta talk Lee/Kirby's FF run, with "The Coming of Galactus" at its heart, and Lee/Romita on Spiderman, particularly "Spiderman No More." Oh, and "Death of Gwen Stacy," obviously.
Walking Dead's Prison arc is a classic; I know everyone got burnt out because of the TV series but that comic was amazing (as was Kirkman's simultaneous work on early issues of Invincible; another artist at the peak of their powers).
Civil War is another great read from top to bottom. "Kraven's Last Hunt."
I feel like I should mention "Crisis," but I have mixed feelings on it as it ushered in the era of "event" storylines that recalibrated continuity, and I kind of blame those for where comics are at today (mostly unfairly, because I know there are much larger socio-economic issues at play).
