So, in no particular order:
Captain America by Ed Brubaker and Steve Epting
This is Captain America as a political thriller. Captain America via Three Days of the Condor. This run does the impossible and brings back Bucky Barnes as the Winter Soldier. It contains the Death of Captain America. It's tense and taut and through it all, Captain America's core remains the same. He is the moral center of the Marvel Universe for a reason.
The Immortal Iron Fist by Ed Brubaker and Matt Fraction and David Aja
Kung Fu Billionaire Danny Rand. That's a great hook. This run includes the pulp predecessor to the Iron First and the battle of the seven capital cities of Heaven. David Aja's art is amazing and the story expands on the Iron Fist mythos in a very genre appropriate method.
Hawkeye by Matt Fraction and David Aja
Matt Fraction takes Hawkeye and puts him in a Rockford Files-esque storyline, protecting an apartment building and its tenants that he has purchased. David Aja takes his art to another level, experimenting with the format in ways that have not been seen before. The deaf issue, the issue from the view point of a child, the issue from the viewpoint of the dog. Issue after issue is consistently excellent.
Daredevil by Frank Miller and David Mazzucchelli
This is the classic run, the one that changed Daredevil from a swashbuckling adventurer to a crime comic staple. The run that brought an edge to Daredevil. The Kingpin, Bullseye, Elektra. To see a man brought to his lowest point and then restored in Born Again. From this point on, Daredevil would have consistently good writing.
Avengers by Kurt Busiek and George Perez
This is the seminal Avengers run. The one that respected the past and forged on to tell at least three of the top Avengers storylines of all time (Ultron Imperative, JLA/Avengers). Kurt Busiek as a writer is able to connect to human emotion like no other. His creator owned Astro City is one of the best comics of all time. George Perez is the master for a reason. His obsession with detail and crowds makes him one of the most sought after superhero artists. He continues to strive to draw larger and larger groups of characters together. To me, when I picture superheroes, I imagine them drawn by George Perez. Classic Avengers stories told by master artists.
Ultimate Spider-man by Brian Michael Bendis and Mark Bagley
Bendis and Bagley were given the unenviable task of restarting Spider-man for the new century. And they stepped up to the plate in a major way. I have cried with this comic. It has one of the best gut-busting page turner laughs I have ever experienced. I love Bendis' writing on a lot of comics from Jessica Jones to Daredevil and the Defenders, and I'm looking forward to his take on Superman. Bagley is another of those quintessential superhero artists. He has worked on Spider-man for so long, that when I picture Spider-man, it is always Mark Bagley. 111 consecutive issues of this team together. For anyone who wants to get a fresh start with Spider-man stories, this is the place to go.
Loki: Agent of Asgard by Al Ewing and Lee Garbett
Al Ewing is proving one of my favorite new writers. With Loki, Ewing was able to explore the importance of stories, as Loki, god of mischief has a chance to start again and morphs into the god of stories. It's funny, it is moving, and it's meta. Lee Garbett provides clean, accessible art, that services Ewing's story very well. A short, but beautiful run.
Unbeatable Squirrel Girl by Ryan North and Erica Henderson
This title reminds us that comics are supposed to be fun. It's not afraid to be silly, stars a very plucky and determined hero in Doreen Green, the Unbeatable Squirrel Girl. It's STEM friendly with Doreen's background as a computer science student, and code has even been used to solve the problems she faces in at least one issue very explicitly. A major component of this title focuses on the fact that Squirrel Girl is not content to just beat the bad guy into submission. She has helped truly turn bad guys around and looks for solutions that don't involve her fists. Highly enjoyable.
Fantastic Four by Jonathan Hickman and Dale Eaglesham
Jonathan Hickman creates very interesting comics. The story goes that when he laid out Fantastic Four, he established essentially everything that would be in his Fantastic Four, Avengers, New Avengers, and Secret War runs. His run is expansive, adding the Future Foundation, the Universal Inhumans, and the Council of Reeds, all of which have been used to great effect. The most important part of the run is its focus on family and the characters. Everything is character driven and grounded in true emotion. It's Hickman's best run so far.
Black Panther by Christopher Priest and Sal Valeutto
This run introduced me to Christopher Priest. I look forward to everything he writes because his style is so distinctive. This book started with a Rashomon/Pulp Fiction style non-linear story, that made it stand out from everything on the stands. Layered and complex plots with political intrigue, corporate espionage, great comic action. Fun new characters. Queen Divine Justice. Everrett K. Ross, king of all white-boys. This run defined the character for years to come. If you like the Black Panther movie, its foundation is here.
These runs to me represent the best Marvel has to offer. I go back to these runs often to enjoy them fresh each time. Each holds up. I look forward to discovering many, many more.