Some Marvel stuff I'd recommend
- Grant Morrison's New X-Men and Whedon's Astonishing X-Men. Both can be read without much prior knowledge, but Whedon's run has some elements from Morrison's. Read Whedon after Morrison for best effect. Remender's Uncanny X-Force is impressive, but doesn't come close to New + Astonishing.
- Garth Ennis' Punisher: MAX. Deeply dark and disturbing, but an absolute must. Read all 10 volumes and From First to Last (collection of one-shots). Ennis also wrote a Marvel Knights run before this, which is pure pulp action comedy and completely different in tone, but also incredible. Welcome Back, Frank is the best Punisher story I've read yet. If you want to read one Punisher arc, make it that one. The rest of his Marvel Knights run is not easy to find in print unfortunately.
- Brian Bendis' Ultimate Spider-man: the only long Spidey run I've read, and I don't feel the need for more. It's good all the way through, but it peaks in the early volumes.
- Daredevil: Miller's Man Without Fear => regular run => Born Again. Then move on to Bendis' fantastic run. Can't comment on Brubaker and Waid's runs yet, but I hear they're also great. Don't think anyone has mentioned Daredevil: Yellow yet, a look at the early years of Murdock with great Tim Sale art.
- Warren Ellis' Iron Man: Extremis feels like the essence of the character in one story arc. I've re-read this over and over, Granov's art is a treat. It's standalone, it's short, read it.
- For Thor I'm a big fan of J. Michael Straczynski's run. It's colleced in one omnibus. It's not finished when he leaves though, so continue with Giellon's issues after. I read JMS after finishing the gigantic Simonson omnibus, and honestly enjoyed JMS' run even more. Coipel's art helps.
- Jonathan Hickman's Fantastic Four is a mind-bending sci-fi epic. One of the best long Marvel runs I've read. Couldn't have asked for a better introduction to FF, and I'm now a huge fan of Hickman. Manhattan Projects and his Avengers stuff are on the pile.
For DC I just want to mention the best Superman stories, since there's more than enough Batman:
All Star Superman
A Superman for all Seasons
Superman: Red Son
Superman: Secret Identity
All these made me a big fan of the character.