There’s a LOT of X-Men comics and most of them are very confusing, but here are some great starting points, depending on what you’re looking for. But watch out: There are a lot of spoilers in here.
If You Want to Jump Into the Current Status Quo
Yesterday's X-Men, the first volume of Brian Michael Bendis and Stuart Immonen's All New X-Men, is the starting point for the current status quo of the monthly X-Men comics. The story starts in the aftermath of Charles Xavier's death at the hands of his star student Cyclops, who is now leading a “mutant revolution” alongside Emma Frost and Magneto. A grief-stricken Beast decides to get back at Cyclops by bringing the five original X-Men to the present so a teenage Cyclops can see what he becomes. Of course, this all backfires horribly, and sets in motion a number of stories that are still playing out every month in Bendis' All New X-Men and Uncanny X-Men series.
If You Want a Brainy, Cool Take on the X-Men
Grant Morrison's New X-Men series was a bold new direction for the X-Men that redefined many core characters while introducing many new characters who have since become mainstays of the franchise. Morrison's clever, sci-fi take on the X-Men is available in many forms — split across three paperback volumes, spread across seven digests, compiled in one huge omnibus — but no matter what, start at the beginning. The first storyline, “E Is for Extinction,” is one of the all-time best X-stories and introduces Cassandra Nova, one of the team's most nightmarish villains.
If You Want to Read X-Men Comics by the Guy Who Created Buffy
When Joss Whedon started his excellent, self-contained Astonishing X-Men series in 2004, he was known as the guy who created Buffy the Vampire Slayer and Firefly, but was still years away from becoming the guy who wrote and directed the Avengers movie. Whedon's take on the X-Men plays to his strengths: lots of great emotional beats, great one-liners, and strong female leads in Kitty Pryde and Emma Frost. This run, which is collected in many forms, is a great place to jump in if you've never read an X-Men comic before, but it's even better if you think of the two volumes as being the two “seasons” following Grant Morrison's three-year epic.
If You Want to Read the Most Iconic X-Men Story
The Dark Phoenix Saga is the most famous of all X-Men stories, and was the point at which Chris Claremont and John Byrne's run on Uncanny X-Men became a huge phenomenon in the world of comics. Some aspects of these comics seem a bit dated today, but the overall story of Jean Grey being possessed by the Phoenix Force and corrupted by the Hellfire Club is a classic, and the basis for many future X-Men comics, cartoons, and movies.