Logan / Wolverine

Flashbacks

 * 1)  Rose O'Hara  First love. Memory of her later erased. (1800s) (Origin, 2001-02)
 * 2)  Clara Creed  - Memory of her later erased. (????) (Origin II, 2013)
 * 3)  Silver Fox  - Killed by Sabretooth (Wolverine, vol. 2 #10,1989)
 * 4)  Raven Darkholme / Mystique  - These two first met and had sex in 1921 (Wolverine, vol. 3 #62-65, 2008)
 * 5)  Seraph  -  Logan fell in love with Seraph due to the manipulations of Romulus (1920s-40s) (Wolverine #126, 1998), Wolverine Origins Annual #1 (2007)
 * 6)  Atsuko  - She died (1945) (Logan #1-3, 2008)
 * 7)  Itsu  - Logan married Itsu, but she died with their expected child. (1946) (Wolverine #40) (2006)
 * 8)  Lin  -  (1950s) (Wolverine: Manifest Destiny, 2008-09)
 * 9)  Native   - During their Weapon X days, Sabretooth convinced Wolverine to track down Native. He did so and they shared a romantic moment... and she became pregnant. Their relationship didn't last long, as Sabretooth killed her. (Wolverine, vol. 3 #13-19, 2004)
 * 10)  Charlemagne  (Spider-Man vs. Wolverine, 1987)
 * 11)  Janet - Wolverine did not meet Janet by chance; Romulus planted her in his life (like he did most of Wolverine's girlfriends) in order to manipulate the man into doing his bidding. Logan was introduced to Janet when he was brought to a training facility in Canada run by Frederick Hudson. While there, Logan was allowed to form a romantic relationship with Janet, who helped "tame" his savage nature. Once they grew sufficiently close, however, Romulus sent the order down to kill her. Their reason for doing so was to teach Logan that any woman with whom he grew close would ultimately meet a grisly death. Wolverine's training officer, Silas Burr, ended up being the one who killed Janet, and afterward, when Wolverine retaliated, Burr plucked out one of his eyes. Years later, when Wolverine encountered Cyber after both men had undergone some form of the Adamantium-bonding process, Logan continued to be haunted by the trauma of Janet's death. (Marvel Comics Presents #87, 1991) (Wolverine Origins #15, 2007)
 * 12)  Pinch  - Wolverine and Pinch were teammates, led by the crime boss Offer. Wolverine was working undercover on the team, but began a relationship with Pinch. When Pinch found out the truth, she abandoned him.
 * 13)  Heather McNeil  (Alpha Flight #33, 1986)
 * 14)  Carol Danvers 
 * 15)  Squirrell Girl  - A past relationship was discussed (New Avengers #7, 2010)
 * 16)  Snowbird  - A past relationship has been teased.

 Main Story 
 * 1)  Jean Grey  (Met in Giant-Size X-Men #1, May 1975)
 * 2)  Mariko Yashida  - Wolverine met Mariko in Japan. (UXM #118, Feb. 1979)

They quickly fell for one another and formed something of a long-distance romance.
 * 1)  Yukio  and Logan shared an attraction that started when he was on the rocks with Mariko. (Wolverine #1, Sept. 1982)

He and Mariko later got engaged. (W #4, Dec. 1982). Mariko broke it off during the ceremony saying, "You are not worthy." (UXM #173) He later learned that the villain Mastermind was behind it all. Wolverine and Mariko's relationship never turly recovered.

The X-Men returned from the first Secret Wars and, accidentally ending up in Japan, fighting a dragon. During the chaos, a young girl named Amiko Kobayashi loses her mother when a collapsing building crushes her. Dying, the woman begs Wolverine to take care of her daughter.Since Wolverine could not take care of her himself, he chose to place Amiko in Mariko's care, whom the girl soon adopted as a surrogate mother. (UXM #191, May 1984)

He later met Charlemagne again, but she died. (1987)
 * 1)  Ororo Munroe / Storm  and Woverine then shared a kiss (UXM Annual  #11)

He later kissed Jean Grey (Inferno, 1989)

His old flame Silver Fox was later revealed to be alive, and the head of Hydra (Jan. 1992)

Mariko became poisoned by an assassin, and instead of dying a slow death, she asked Wolverine to kill her. Wolverine did so. (Jul. 1992)

Silver Fox waas later "killed" again (Wolverine #60-64,1992)
 * 1)  Caley Blair  - Killed (Wolverine/Punisher: Revelation #1-2, Jun. 1999)
 * 2)  Amir  - Killed (2006-2007)

Logan was reunited, poorly so, with Lin, she having become the crime boss Black Dragon (Wolverine: Manifest Destiny #1-4, 2008-09)
 * 1)  Cassie Lathrop 
 * 2)  Remus 
 * 3)  Rose Carling Wu 
 * 4)  Ai-Chia Wong 
 * 5)  Elektra 
 * 6)  Tyger Tiger 
 * 7)  Gahck 
 * 8)  Domino 
 * 9)  Pink Lady 
 * 10)  Lynx 
 * 11)  Felicia Hardy / Black Cat 
 * 12)  Natasha Romanoff / Black Widow 
 * 13)  Melita Garner -  A reporter who Wolverine first encountered while the X-Men were living in San Francisco. Logan saved her from an armed mugging. (Wolverine: Weapon X #1, Jun. 2009) This piqued her interest and she began prepping an expose on the most mysterious of the X-Men. Logan initially began working with her in the hopes of developing a contact in San Francisco. Their relationship soon blossomed into something serious, despite Logan's efforts to dissuade her from getting involved with him. (#9, Mar. 2010) He disclosed a great deal to her about his past relationships, so that she would fully understand the dangers of being with him. She was more than willing to take her chances. Melita survived being attacked by Logan's enemies and helped save his soul from Hell. They were happy for a time and dated for 13 months.

During this time, Logan killed Mystique during an encounter. (2011) She later was resurrected from the dead, looking for revenge. (Wolverine, vol. 2 #300, Mar. 2012)

When Melita received photos of Logan having sex with Yukio (actually it was Mystique in disguise) she broke things off with him. (W#304, Jun. 2012)

Despite the love she felt for him, she realized that he was not the monogamous type she was after. She has since joined Seraph's Angels, a group comprised entirely of Logan's ex-girlfriend. (This group was revealed in Wolverine, vol. 4 #20) - (UXM.net)

Logan later began an somewhat undefined sexual relationship with Storm. (Wolverine and the X-Men #24, 2013)

Sexual, not at all Romantic

 * 1)  Typhoid Mary 
 * 2)  Viper 

Age of Apocalypse

 * 1) Jean Grey

Earth 9811
House of M 		Mystique
 * 1)  Storm  - The two are married with a daughter named Kendall

MC2

 * 1)  Elektra - Married with daughter, Rina, AKA Wild Thing

Mangaverse

 * 1)  Felicia Hardy / Black Cat 
 * 2)  Lady Deathstrike  - Hinted at.
 * 3)  Sue Storm / Madame Hydra 
 * 4)  Viper 
 * 5)  Gaea 

Ultimate

 * 1)  Storm 
 * 2)  Jean Grey 
 * 3)  Magda 

What If?

 * 1)  Red Sonja 

Old Man Logan

 * 1)  Maureen 

Other
 X-Treme 
 * 1)  Witchblade  - Married
 * 1)  Hercules 

Animated Series

 * 1)  Lady Deathstrike 
 * 2)  Jean Grey  - The same dynamic applies as in the comics.

Movies
At the end of that film, she apparently sacfices herself to save the team. She turns out to have survived, but her powers have increased and made her take the insane form of her persona called the Phoenix. Her first act as the Phoenix is to murder Scott. Althoug she later kills Professor Xavier (who later turns out to have survived) and joins Magneto's evil mutants, Logan refuses to believe that the real Jean is still within her. After the climactic battle, with her powers going crazy and destroying everything in sight, she begs Logan to kill her, and he does so. This decision haunts him for some time to come.
 * 1)  Kayla Frost  - After leaving behind a life of violence in a special secret military team, Logan, in the 1970s, falls in love with this schoolteacher and settles down for a normal life. It later appears, however, that his psychotic brother and former teammate Victor, AKA Sabretooth, has come and killed her. In his quest for revenge, he allows his old boss Col. Wiliam Stryker, to bond his skeleton with the metal adamantium. He then finds that Kayla is alive, and that she was part of a plan of Stryker's and Victor's  to get Logan to have the procedure done, as an experiment. She begs his forgiveness, revealing that she was forced to take part in the plan, as they had her sister captive, but that she truly did fall in love with him. Logan forgives her, and the two plan to resume their relationship, but in the ensuing battle against Stryker, she is killed. Whatsmore, after being shot in the head with an adamantium bullet, Logan's memories of his entire life up to that point are eliminated. (Years later, though, he appears to get them all back) (this character is claimed to be an adaptation of Silver Fox, despite how little they bear in common. She does not even have the same powers as Silver Fox, instead having an ability to make people do what she tells them upon touch).
 * 2)  Jean Grey - As in the comics, she and Logan form a strong connection when he joins the X-Men. In the second film, this progresses to a kiss, but she still chooses to remain with Scott.

Logan later participates in events that change the timeline from 1973 (ten years before Jean and Scott joined the X-Men) onward, before awakening in the alternate version of the present that he created, but has no memory of.

In the new timeline, in 1983, we see Jean and Scott first join the X-Men and meet each other, and the buddings of their romance. She also meets Logan for the first time, as she briefly manages to calm him down after witnessing his berserker rampage, only to have him flee into the woods.

When Logan awoke in the new version of the present, he finds both Jean and Scott alive, and in a relationship, noting "It's nice to see some things never change." Also, in a deleted scene from X-Men: Days of Future Past, Storm and Wolverine are shown to be in a relationship in the apocalyptic future, before Logan goes back in time and changes it.
 * 1)  Mariko Yashida  - Logan and Mariko fell for each other during his adventure in Japan, but he then left to pursue other ventures.