Batgirl (2000): Cassandra Cain's mother passed her to her father literally at birth, who in turn shot the midwife dead and took the infant to be trained as the ultimateassassin in isolation from spoken language. Given that said mother became known as Lady Shiva, it is hard to imagine that her influence would have helped...and the kid seemed to have turned out emotionally together enough to run away from homerather than kill...again... at least until she's forced to kill Shiva herself. She got better.
Batwoman lost her mother in a hostage situation when she was a kid. She also lost her twin sister...or so she thought.
Both of Tim Drake's parents spent a lot of time traveling the world while he stayed at home in Gotham and eventually both of them were murdered but his mother died first by about a year leaving just him and his dad as the surviving Drakes by the time Tim's solo series Robin started.
Cardboard: Cam's mom and Mike's wife, Carol, died before the story begins.
Matt Murdock, aka Daredevil, was raised entirely by his father (this turned into Parental Abandonment when the guy was murdered in the first issue of Matt's series). His mother went completely unmentioned for over twenty years before finally showing up out of the blue; turns out that she abandoned her child to become a nun. Original Sin later revealed that she abandoned him because she was hit with a major case of Post-Natal Depression that drove her to nearly kill him. She was so horrified of the actions that she ran away. Darkdevil, Daredevil's Legacy Character in Spider-Girl, also has a missing mom and a dead dad. It's implied that Mom is still in jail for killing her abusive father. At least, that's what Darkdevil hopes.
N'Dare Munroe and her husband David were killed when terrorists bombed the building they lived in, orphaning their daughter Ororo.
Brian Fies' Whatever happened to the World of Tomorrow is more about the world at large than the unnamed main characters, but the fact that the son's mother is never ever mentioned stands out like a sore thumb when it's heavily implied his father is serving in WWII - so who is taking care of the teenaged or pre-teen kid?
Kate Bishop's mother died some time before Young Avengers started. So did Teddy's, though he didn't know it for years, and then the woman who raised him burned to death in front of him.
Happens to both of the heroes in Quantum and Woody. Quantum's parents went through a divorce after an auto accident, and she happily left after securing a huge alimony payment. Woody's mother divorced out of an abusive relationship and became an impoverished drug addict, emotionally absent as she left Woody to fend for himself.
Jessica Jones parents and little brother were killed in the car crash that gave Jessica her powers. She was adopted into a loving family (the mother had been adopted herself at a similar age), but except for flashbacks, she isn't seen in Alias. Her adoptive parents both finally make a real-time appearance in The Pulse.
In Seconds, Katie talks to her father on the phone, but her mom is never mentioned. It's implied she died from an unspecified illness.
In Violine, Violine's mom turns out to be missing and Marushka, the woman who adopted her, turns out to have lied about being her mother.
Kenton's mother in White Sand is absent, presumably having returned to the Darkside after bearing Praxton a child.
Wonder Woman (1987): Natasha Teranova is a missing mom, and it breaks her heart that her daughter will likely never know what has happened to her and regrets that she didn't spend more time with her before the mission that went haywire and ended with her lost in space. She makes daily recordings for her daughter just in case the messages can eventually be given to her.
Prior to getting hit with a Continuity Snarl so bad she has her own pageWonder Girl Donna Troy always wondered about her birth mother, only knowing she'd been rescued from a fire by Wonder Woman as a toddler and raised on Themyscira with only the vaguest of memories to go on. In Who Is Donna Troy? Dick Grayson was able to help track down Donna's past and discovered Donna's birth mother Dorothy Hinckley gave Donna up to an orphanage when she learned her terminal cancer would not let her be a parent to her little girl for much longer.
Wonder Woman: Warbringer: While Theo's dad shows up at the kind of event you'd expect him to bring his significant other to and is talked about quite a bit his mother doesn't even get a mention.
In Zodiac Starforce, Emma's mother is implied to be one of the casualties of the girls' battles with Cimmeria.