I noticed last year, when I was watching at least six 1-hour TV dramas a week, that almost every story you run across has a character with background problem's with their father. Occasionally you'll see characters with mother-problems, but more often, if a character doesn't have father-problems, they have a bad relationship with both parents. When I tried to explain my findings, people just asked what strange shows I watch, so I've decided to prove it. This next bit is quite long, so feel free to just skim.
FOX
24 - I stopped watching this on Day/Season four or five, I think, because it was getting way too violent, and up to that point we didn't know anything about Jack Bauer's parents. However (spoilers
Bones - I follow this religiously, so I don't even have to look up the plot. At the start of the show, we learn that protagonist Dr. Brennan's parents left her and her brother at Christmastime and have been missing ever since.(Spoilers
Fringe - I started watching this recently. It's about a woman (whose father is never mentioned and whose stepfather was abusive) investigating sci-fi level occurrences in New England, who attempts to enlist the help of a "Fringe Scientist" Dr. Walter Bishop. Unfortunately, he's in a Psych Ward, and can only be called out by family. His wife is dead, and his son, Peter, kinda hates his guts. She talks/blackmails Peter into getting Walter out, and he spends a few episodes complaining about how stupid and unrealistic everything they're doing is (I don't mean to sound like I dislike his character - there were times when he was the only realistic person in the cast). And while Peter eventually learns to get along with Walter, he still has to cope with the fact that Walter's a psycho who preformed experiments on kids. (Spoilers
Glee - I don't watch this, but I hear it's popular. Here are the important ones: Rachael (That front row chick) has two dads, a married gay couple who mixed their sperm so she doesn't know which one is biological or not. Finn (The singing jock)'s dad died is Operation Desert Storm. Tina (The goth) describes her dad briefly as an Asian Vampire. Kurt (The gay kid) is pressured by his dad to act masculine, but the dad eventually sticks up for his sexual orientation (Go, dad!) There are more fathers in this drama, but none that I see any reason to note.
House - An interesting medical drama that I just never got around to watching much of. According to wikipedia, however (spoilers
Lie to Me - Another show I used to watch. The protagonist's father hasn't really been mentioned yet, though his mother committed suicide. However, he does have a daughter who takes a disliking to her dad's abilities to read people's emotions.
ABC
Better Off Ted - A comedy that I never watched, though it looks mildly appealing. This is similar to Lie to Me in that, as far as I can see, the only father issues are between the protagonist and his daughter.
Brothers and Sisters - I never watched this show, so I can't give any spoilers, but according to my research this show starts with the death of the family patriarch, William Walker. His death reveals some secrets he has been hiding and sheds light on other family secrets, and kickstarts the plot of the show. Obviously there are problems around him, most notably his affair.
Castle - A relatively new show that I watch because of the witty writing and literary allusions. The protagonist, mystery writer Richard Castle, doesn't even know who his father is because his mother... well... Anyway, he has a good relationship with his daughter, though she tends to be the responsible parent a lot of the times.
Grey's Anatomy - Never really got into this show, but apparently people like it. From what I can tell, (spoilers
Lost - I'm not even going to touch all the characters here, because there are soo many. Here are the top three protagonists, however: (spoilers
Private Practice - A spin-off of Grey's anatomy. The protagonist here reveals to the audience that her father was adulterous and spent time with her only as a pretense.
NBC
Chuck - A relatively under-appreciated show that we started watching because they advertised at the store my brother was working at. In this show, the protagonist, Chuck, is kind of a loser, working a dead-end job and living with his older sister and her fiance, until he gets government secrets programed into his head. He explains first season that their mother died when he was young and their father disappeared soon afterwards. We have a negative view of the father here, who left his children, (spoilers
Friday Night Lights - Apparently a pretty good show that never really appealed to me. From what I can see, the protagonist, the football coach, takes on the role of surrogate father for his team players. I could probably go down the entire team line-up, but they're basically all similar, boys with unsupportive parents or fathers who abandoned them (not all, of course, but a significant amount).
Heroes - I watched this for a few seasons until I realized that I really didn't care anymore. The enormous cast frequently flip-flops between good-guys and bad-guys, but here are some of the headliners: Claire, the 'cheerleader', is adopted. Her adoptive father is made out to be a bad guy for quite a while, though he then becomes a good buy who does some bad stuff. Her real father (spoilers
Law and Order - An enormous franchise that I never got into. Minimal research on the main characters reveals that Jell Goldblum's character shuns his parents' profession, refusing to speak to his father though they live in the same city. Another protagonist, Elliot, implies that his father is abusive, and his partner Olivia was born after her mother was raped. I'm sure there are more, but the franchise is so wide that it might take a while to track them down.
The Office - The US version of this show always looked good, but we never get around to watching comedies in my house. Though comedies tend to shy away from serious childhood backstories, Steve Carell's character mentions coming from a broken home.
If you managed to read through all of that, I commend you.
I might have seemed to be making a negative statement about fathers, but quite the opposite. When I realized that fathers, and particularly the bad father-child relationships, were so prominent in modern fiction, I tried to reason why this might be, and this is what I've come up with.
Approximately 50% of American children live in a home without a father. While the divorce rate has decreased in the past few years, the percentage of women giving birth outside of marriage has increased. Couple that with statistics that show that the majority of children who drop out of school, run away from home, join gangs, participate in violent crime, and/or end up in Juvenile Hall come from homes without a father, we can see how this may be a problem. Of course not every kid with a deceased father is going to end up failing at life, but denying a child a father certainly doesn't do anything to help them.
I'm not trying to make some political statement, I'm trying to restate what I've noticed. The father complex is popping up more often in fiction (Shown here through TV dramas, but this also includes movies, books, and anything else), and I believe this is a reflection on the person experiences of the producers making our fiction. More writers grow up without fathers, and subsequently more characters do, too. I find it fascinating that this subtle niche of society has made its way into storytelling - not that it's anything new. Stories attempt to tell truths, and if it's true that this occurs frequently, then it will wind up in stories.