From the top of my head:
1.) I really liked Jean in the Onslaught saga, or better mainly during the set up/first arc of the event. She had some amazing showings: Onslaught visiting her and tries to get the secret out of her how she became Dark Phoenix. I also liked the scene when Jean goes shopping and she hears all these ugly and angry opinions in the thoughts of the humans she meets on her way. She was also the emotional starting point for the event with the video from Bishop's future warning everyone about a great threat and that the X-Men have been betrayed. I also liked her use of telepathy when she suppressed Bruce Banner's personality within Hulk at the end.
2.) Her entire storyline with Sabretooth at the mansion is pretty great. She questions Xavier's decision, kicks Sabretooth butt repeatedly ("You are a firecracker but I'm an atom bomb"), and is also hunting Sabretooth down when he finally escapes and indents to kill Generation X.
3.) Her powers in Claremont's X-Men: Revolution is just stunning to me. They brought the Phoenix effect back as a manifestation of her psy powers without attachement to the "cosmic retcon bird".
4.) In general, I really adore her friendship moments with so many X-Men in the 90s. There is a moment where she flies with Arcangel during/before Phalanx Covenant. Or hugging Quicksilver in the kitchen after the events of Onslaught. Taking are of Jubilee when she is afraid of Sabretooth, etc. etc.
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But I mainly started to love her during Morrison's run and after. That is the ultimate Jean Grey for me. She starts to become truly an Omega-level mutant again after the Dark Phoenix Saga.
Her scene in Duggan's X-Men helping Synch understanding her telepathy is also pretty quintessential to me. I think Jean's empathy is the core to understand the character. Some psys turn bitter and manipulative (Emma, Xavier) because of their powers but she (somehow) keeps her trust in humanity despite her knowledge about every dirty secret human's have and she becomes the ultimate empathetic Healer.
Hence, when she psychometrically cleans Xavier's mansion after Bastion's attack, meditation upside down, is my absolute favorite Jean Grey moment.
Bam. Done.