Gonna have to echo some others and pick these three
1. Dark Phoenix Saga (really the Claremont/Byrne era as a whole, but this is the heart of it)
2. E is for Extinction (the whole first arc up to Nova's defeat)
3. House of X/Powers of X
Also love Mutant Genesis. Not the greatest X-story by a long shot, but it's neat to see almost every major X-Man (minus Kitty, Kurt, Rachel, Alex and Lorna) gathered together with some great early Jim Lee art against their most iconic nemesis.