Interesting.

Wow, what a tough question.  There are so many great choices and stories, I really can't boil it down to just one. So here's a few:

Dark Phoenix is the pinnacle, without a doubt. 'Nuff Said

Not really a storyline per se, but the original Brood Saga which led into the quasi-sequel to Dark Phoenix (#162-176) The team in a space horror movie, their first meeting with the New Mutants, Rogue joins, Mastermind returns, Ororo goes mohawk (and takes a big step on her path as leader by becoming nominal leader of Morlocks) and a wedding no less. All wrapped up in terrific Paul Smith art.

The Asgardian Wars event (X-Men/Alpha Flight #1-2, New Mutants Special Edition #1, UXM Annual #9) A cool team-up with Alpha Flight and mutants in a fantasy setting.

The X-Cutioner's Song crossover event. I thought the base emotions involved here (anger, expectations, despair and disappointment, respect) made this event better overall. The trading cards helped too.

Fatal Attractions crossover. While it may have set up the awfulness of Onslaught for later, this event had tense drama, fierce action, and lasting consequences for some characters. Plus, perhaps one of the strongest views/looks at the Xavier/Magneto frenemy dynamic. (Really, Lobdell and Nicieza are so underappreciated. As Miller overshines everyone on DD, Claremont overshines all on X when this duo crafted some fine stories).

And for sheer scope, scale, effect, style, and lasting impact, Age of Apocalypse.

Sometimes I'm amazed that you and I are friends

Wow, it's like I could have written this post.  :-)

The Jubilee/Prof X rollerblading issue and the death of Illyana were two of my favorite issues.  And that's pretty notable considering that I think that there wasn't too much that I liked about the X-Men after Claremont's departure.  And the post-Dark Phoenix issues were also some of my favorites as well.  In particular, the issue where Kitty defends the X-Mansion against the N'Garai demon, and the story when the X-Men have to rescue their loved ones from Dr. Doom and Arcade, and Storm gets turned into a living statue.  I think there was something powerful in the way Storm was brought to her senses after she started turning into sort of a Dark Phoenix version of herself by remembering what happened to Jean.

I find it difficult to choose one particular storyline, but the Brood Saga is definitely up there. Unlike most members here, my favourite X-Men issues are not from the late seventies, but rather from the early to mid eighties, when Kitty was first on the team. To me, her inclusion made the X-Men a bit more light-hearted, even if there were plenty of dark issues (like the ones featuring D'Spayre or Belasco). It's telling that her removal from the book (as well as Nightcrawler's) coincided with the Mutant Massacre and the shift toward "grim and gritty" stories.

There are two double-page spreads by Cockrum in the Brood Saga that really wowed me; the first is when the Brood Acanti ship swallows the already quite large Starjammers' ship, and the second is when the X-Men see the giant Acanti corpse that serves as the Brood's city on their home planet.

There are also so many nice character moments and development, like Storm's distress at being far away from Earth, Cyclops reconciling with his father, and Kitty and Peter acknowledging their feelings toward each other. And not to mention Logan walking in on Kurt praying, and the little conversation that follows between them.

And note that the conclusion of the Brood Saga precedes Aliens (and the concept of there being a 'Xenomorph' [sorry RR, I know you hate the term] hive society with a queen at its lead) by three years!

Agreed! It was fun seeing the team bonding and building their friendships with little tidbits given here and there throughout the story-line giving them more depth of character. It was 98 that grabbed my full attention and pulled me into wanting to continue with the team. And Cockrum was hitting it out of the ballpark with his art making the merry mutants individualistic and stylish. Claremont hadn't as yet gone off the deep end with too much of making them "his own" so it all felt more real and fresh than later on when he was more prolific with his authoritative writing.