Cosmic Dash features Dash's father, Razaar, who apparently vanished, is currently hunted, and whose son is now hunted in order to lure him out. Not a pleasant guy, either, as he has eviscerated an attacker in front of his son, and was last seen with a mysterious race mentioning an expedition.
Count Your Sheep has a Disappeared Dad in the form of Marty who we only ever hear about in flashbacks or wistful reminiscences. He's explicitly dead, though.
In The Dreamer, Alexander's dad left the family (or rather, his mom kicked him out) when he was about 10 years old. He's never seen him since.
Kimiko's father hasn't really been around much in her life in Dresden Codak, aside from giving her a bunch of money when her mother died.
In Fans!, many of neurotic Ice Queen Shanna's issues stem from the fact that her father abandoned her and her insane mother when she was just a child. Unlike many of the fathers on this page, however, when he does finally appear he's treated somewhat sympathetically; whilst his abandonment of his wife and daughter isn't condoned he's depicted as an uptight-but-decent man who just snapped under the pressure of his life and later genuinely regretted his actions, but felt too ashamed of himself to return.
In Girl Genius, both of Agatha's biological parents and her uncle Barry have been missing for years. Her mother Lucrezia has since reappeared (sort of), but given that Lucrezia is also the Other, Agatha would probably have been better off if she had stayed missing.
Gilgamesh spent his early childhood knowing nothing about his family. He was stunned to learn that he was the son of Baron Klaus Wulfenbach, iron-fisted ruler of Europa—from Klaus himself. He was kept in the dark for his own safety.
In El Goonish Shive, Susan's father left after being caught cheating and going through the ensuing bitter divorce. Neither Susan nor her mother handled it very well.
In Gunnerkrigg Court Annie's father left her and her dead mother shortly after his wife passed away, without telling anyone where or why. He has refused to contact his daughter since. It is stated, though, that this behaviour isn't exactly new for him... In Chapter 51, he takes a position at the Court, and seems just as distant as when he wasn't there at all.
In The Inexplicable Adventures of Bob!, the first time Molly ever hit anybody was when Galatea taunted her for not having a "real" daddy. (Molly felt very guilty afterwards for hitting her.)
In Jupiter-Men, Jupiter-Man vanishes inexplicably without warning, with the Star Seed appearing at a construction site before being absorbed by the Avalon twins. His absence leaves his son Nathan struggling to keep up with his role as a Star Guardian until he discovers that Quintin and Jackie have Jupiter-Man's powers.
Lighter Than Heir: Zeppelin is angry at her father for failing to return. Finding out just what happened to him, that he was tortured to death and vivisected by Zamoran Scientists, is even worse.
Jodie's father (from Loserz) is missing, as told here.
In Misfile, Emily's father disappeared before she was born, never to return. His only contribution to the plot (apart from Emily obviously) was to ensure Emily's mother became the Education Mama we all know and...er...know.
Narbonic both inverts and averts the trope, as the first time we hear about Helen's father it's implied Helen's mother served him for dinner, and then once the truth is revealed, we discover there never was a dad — Helen is a clone; it turns out to be a Should've Seen That Coming due to the fact that Helen's mother is a Mad Scientist.
Neko: The Cat: Michiko's father vanishes soon after they move to the countryside, apparently due to his job. As the stepmother points out though, emotionally he had vanished long before then and offered no support after her mother's death (which Michiko had witnessed at the age of 10).
Eiji of 9th Elsewhere; he claims to see his father at family dinners once in a while, but his mother points out that he hasn't been to one in months.
In The Order of the Stick, Elan's father was one of these, until recently. Haley's father has apparently been kidnapped. Roy's father, however, has been quite active in his son's life, even though he's dead.
Eugene is an interesting case. It seems that he wasn't active in Roy's life until he died; prior to that he seems to have been quite neglectful, was bitter that Roy became a fighter instead of a wizard and showed clear Parental Favoritism to Julia. However, he specifically passed up a chance to defeat Xykon because it would have involved abandoning the family and possibly putting them in danger, but specifically lied to Roy saying he would have left them if given the chance.
Haley's reunion with Ian was contentious, since she's abandoned the paranoia-happy way he tried to raise her. However, they smoothed things ago again before the plot went on from him.
A flashback reveals that Durkon's father died in battle before his mother even knew she was pregnant. After learning that he fathered an illegitimate child with Hilgya, he asks for her hand in marriage the second he has the chance so that his own son won't have to grow up without a father.
Heartful Punch of Sleepless Domain is currently estranged from her father because he disagreed with her becoming a Magical Girl, and seeing how her mother and grandparents are dead, it means she lives in a boarding house the M.G.S.I. has set up for other girls in her situation.
In Strays, Meela's father never appears; she also dreams of a boy whose father was murdered.
In String Theory (2009), Dr. Schtein has an estranged daughter named Alice. Schtein's father also died soon after he was born.
Unsounded: Jivi's mother is at sea but she was seen in the dream Jivi was having when he was introduced, and is mentioned a few times, he brings up the uncle he was living with before running but his father isn't mentioned. At Litrya Shrine someone finally asks after his father, and his response is that his dad is "super dead".
Witchy opens with the main character's father being executed.
It Was a Gift: she received it just before he disappeared.