Before we get to the number one pick, lets take a moment to look over the list:
Jean Grey/Pheonix
Before I get started, I need to remind you exactly what this list is here to express. This is not just a list of my favorite X-men, it is also about the contribution the character makes to the story of the X-men, and the Marvel universe. While Jean may not be my favorite character, there is no denying that she is the most important person involved with the team.
Jean discovered her telepathic powers when her best friend was killed in a car accident. Jean shared her friends death and basically shut herself off from the world. Worrying about their daughter, Jean's parents contacted their friend, Charles Xavier. Being a telepath himself, Professor X was able to block off Jean's telepathic abilities to help her maintain her sanity.
Although she was Xavier's first student, she was the last addition to his X-men. She made a big impression on the boys, and quickly earned their respect. Her powers were an important part of keeping the team alive and winning battles.
As with all of the X-men, Jean's powers grew over time. She also began to be involved with Cyclops. Jean took the code name Marvel Girl. (More accurately, it was handed to her by Professor X.) After 'graduation,' the team shifted from the school uniform to something a little flashier. After the expansion of the team with the addition of the new X-men, Jean decided to stay with Scott and the ream. This led to the biggest event in Jean's story.
The X-men had borrowed a space shuttle to battle Magneto on his asteroid base. The team was fleeing, but the systems were pretty much shot, and they were flying into a radiation storm. Someone had to pilot the vessel, and after knocking out Scott, Jean was the one for the job. She used her reawakened telepathy to learn how to fly the shuttle and, after locking her teammates in protective cells, flew the shuttle with only her telekinetic shield as protection.
After crashing in the bay, Jean emerged from the water declaring herself to be Phoenix. Over time, Jean showed a massive increase in power. she could rearrange the molecules of her clothes, stop Scott's eye beams from leaving his eyes, and even travel through space. It was later revealed that during those final, desperate moments, Jean had connected with the galactic force known as the Phoenix force. It was feared throughout the universe, and with good reason.
As the Phoenix, Jean (actually the Phoenix Force using her form while the real Jean was in a healing cocoon at the bottom of the bay) helped to save the universe by healing the fractured M'kran crystal.
Things started to get complicated for Jean when the X-men had supposedly been killed by the destruction of Magneto's underground base. (They got away, but were out of contact for a long time.) During that absence, Matermind was using his illusion powers teamed with the Hellfire Club's White Queen, to corrupt her mind. She had illusions of living another life where Mastermind was her husband. When the X-men battled the Hellfire Club, Jean was revealed to be the new Black Queen of the organization. In the struggle to free Jean's mind, a hunger was unlocked and after the battle, Jean took off into space.
Overwhelmed by a hunger from the Phoenix force, Jean flew off to an alien sun and destroyed it, killing the population of an entire world. The Shi'ar empire threatened to kill Jean, but Professor X suggested that they try to contain the power of the Phoenix force. They were not able to make this work, so Jean was sentenced to death. Facing Jean's destruction to protect the universe, the X-men faced the Shi'ar Impreial Guards in a battle on the moon. Jean's personality surfaced enough to activate a laser in the battle area that killed her.
Later, Jean emerged from her cocoon and the original X-men were reunited to form X-factor. During her absence, Scott had married a woman named Madelyne Pryor, who was actually a clone of Jean. This clone ended up becoming the Goblin Queen during the Inferno storyline.
Jean is probably best known for her frequent deaths and resurrections. I'm not even sure how many times this storyline has been used, but currently she is dead, but who knows for how long.
Although Jean and Scott never had any children, they still have a family. Scott and Madelyne had a son, Nathan, who was whisked away into the future and became Cable. Also, in the Days of Future Past storyline, Scott and Jean had a daughter, Rachel, who had been kidnapped and turned into a mutant-hunting hound. She was later deprogrammed by the future X-men, and Rachel's connection to the Phoenix force was used to send Kitty back in time.
Due to a temporal anomaly, Rachel not only survived the change in the timeline when Senator Kelly was save, but she also found herself in the present. After joining with the X-men for protection, Rachel tapped into the power of Phoenix and used that power to fight with her friends.
Who knows what the future holds for Jean and the Phoenix Force, but personally I miss them both. Hopefully Jean will return soon.
PS I recently saw that something temporal happened and brought the original X-men from the past into the present. I'm not sure what that means for the team, but it looks interesting if nothing else.