Nature Versus Nurture

Everyone knows about some of the fundamental questions to life - who are you, what do you want, where did you come from, and where will you go? Those are the "what" questions, but this is the "why". Why did you say that? Why did you do this? Why were you there?

Innate qualities and personal experiences both play an important part in determining or causing individual differences in physical and behavioral traits, but this raises the question - which was more 'responsible' for such traits? Were these Abusive Parents abused themselves, and take that out on their own kids, or were they always malicious to begin with? Is the concept of free will (i.e. truly independent thought and truly independent decision-making) valid, or are your decisions brain-made "echoes"? Are your personalities determined more by genes, are they influenced your own experiences, or are they made so that your personality truly is unique?

At any rate, fiction can have a field day with this, and depending on the writer, it can skew to either side of the argument. Upbringing Makes the Hero is a sub-trope.

Anime and Manga

 * In Elfen Lied, a point is made about whether or not the diclonii really are malicious, or if their cruelty is a byproduct of how they were raised. Lucy appears to be the latter; Mariko appears to be the former. Note that neither side is plausible in the manga.
 * Naruto has Sasuke, Gaara and Naruto; their personalities and mindsets were influenced by their upbringing, but whereas the former two dealt with it badly, the latter was able to pull through because he was luckier than the others, though he convinced Gaara to change his view on life, and hes trying to do the same to Sasuke.
 * There's a lot of In the Blood going around, in that Sasuke's family has a long habit of choosing 'power' over 'strength' that supposedly goes back to the ancient founder of their clan, the elder son of the Sage of the Six Paths. Doujutsu and sociopathy apparently have a causal link, though not an inescapable one.
 * On the other hand, Gaara apparently had  and a cold bastard of a father, and to compicate matter was raised by an uncle who was very kind and looked just like his mother. And was also ANBU and accepted the mission of making a hit on the six-year-old boy he'd raised,
 * And despite never knowing them, Naruto is just like both his parents.
 * In One Piece, comparisons between Luffy and his various rivals are made throughout the series, notably with Crocodile and Moriah. The latter two became who they are due to a rather screwed-up chain of events, while Luffy remains who he is because he apparently chose to be.
 * Crocodile has a backstory?
 * Everyone in One Piece has a backstory.
 * The Akumetsu are several dozen clones made from an extremely evil guy as part of a project to assure his immortality, all separated as infants and raised in may households across Japan, all under the first name Shou and all but one unaware of the others. They are nothing like their original DNA donor, apart from a possibly-related mad indifference to normality. They are, however, so much like one another they very nearly have a Hive Mind within a weeks or even days of banding together.
 * I.e., both sides of this trope are being used and abused with reckless abandon.
 * Note that they did start swapping important memories around pretty early, though not many. To a certain extent they all imprinted on the Shou who inspired the whole Akumetsu project, but even before that they were so alike it's creepy, and honestly that Shou is less like the others than any of them.

Comics

 * Brought up in most depictions of Superman: Superman is Kryptonian, but was raised by kindly old adoptive parents. In older stories, it was usually implied that his superior Kryptonian heritage and abilities were the cause of his strict moral compass, but in latter stories (especially after other, villainous Kryptonians, were introduced), it's outright stated that Superman's upbringing is responsible for creating who he is.
 * During his Darker and Edgier interpretation, Superboy was all about this trope. Superboy is a clone created by human DNA that was altered and/or combined with Superman's DNA (Depending On the Writer). In the earliest years, his "daddy" was Paul Westfield and later, it was retconned to be Lex Luthor instead. Neither of them are very nice people. So, Superboy constantly questioned whether he was destined to become good or evil based on the genes provided by Superman or his human father.
 * In his New52 incarnation, Superboy is flat out amoral. The group that cloned him outright questions whether his lack of human empathy is due to being a clone, being half alien, or lacking Superman's overall upbringing.
 * Nooooooo! CONNNNNNN !

Literature

 * Isaac Asimov used this with regards to robots, of all beings, in the short story compilation/narrative I, Robot, by comparing physically and positronically identical robots who developed with different frames of reference (generally resulting in aberrant behavior).
 * We Need to Talk About Kevin is based around the nature/nurture debate -- did Kevin grow into a murderer because mummy didn't love him enough, or was he a psychopath from the word "go"? Basically, it weighs up blaming the mother when her child grows into someone diabolical, against the disturbing idea of being born evil.
 * Worldwar (Literature) features aliens raising humans, and humans raising aliens, in order to see how close they can make each species to their own.

Live Action Television

 * The entire plot of Trading Places begins when the Duke brothers place a bet on which is true.
 * Long before Trading Places, two businessmen tested this on The Three Stooges in "Hoi Polloi".

Western Animation
"Brock: Our parents may have died together, but you had your precious aunt and uncle. We had no one, we've always been alone... until now."
 * This was the title of the season one finale of The Spectacular Spider Man. It concerns the different upbringings between Peter Parker and Eddie Brock.

Universal Media

 * Inevitably brought up in stories involving:
 * Cloning Blues and Evil Twins.
 * Time Travel stories invoking For Want of a Nail and Butterfly of Doom.