Within the Iron Man.
Onscreen in the Marvel Cinematic Universe, Tony Stark is portrayed as lacking the love and affection of his father, who has long been dead before Tony built and donned the Iron Man armor. Both of Tony's parents, we learn, were in fact killed by the Winter Soldier --- a brainwashed Bucky Barnes, Captain America's closest friend --- under orders of HYDRA. This rift further compounds the contentious relationship between Captain America and Iron Man, which takes several more films to repair.
The Stark parents of the comics suffered a similar fate to their cinematic counterparts, but under considerably more mysterious circumstances. Maria and Howard Stark had met while Maria was in a relationship with Obadiah Stane, leaving him for Howard after a long period of discontent. Together with Howard, she'd leave Obadiah, and together the two would run off and try to start a family (to varying degrees of success...it has gotten very complicated). As Howard was already running Stark Industries by the time they met, they were never for want, and had considerable clout, power, and wealth. They were at the height of culture and influence by the time Tony Stark had come into their lives, and their deaths shaped both their son's life, but also the society in which they'd lived. As with the MCU, both Howard and Maria Stark were killed in a car accident. The particulars of that fateful accident, however, differ greatly. While there is a definitive answer as to what exactly happened to the Stark parents in the films, their is much ambiguity as to who is responsible for their deaths. Three prevailing theories exist to explain who had killed Tony's parents:
Hydra is the global supervillain and terrorist organization that is a constant foil for most of Earth's superpowered heroes, and is most consistently rumored to be responsible for the Stark parents. Howard Stark had run afoul of Hydra during World War II, where he had been captured and tortured by the Red Skull to reveal the secrets of the Manhattan Project. Through his work with the US government, he and stark Industries were involved in developing the Captain America Project and super-soldier serum, as well as the Arsenal robots, which were later kept hidden in a subbasement of his mansion. Running afoul of the Red Skull specifically put a target on Howard's back, and it has been suspected that he, and the organization, were the instigators of the deaths of the Starks.
V-Battalion was a World War II group that initially fought against the Nazis. Led by Citizen V, the Battalion ran afoul of the Nazis, and, specifically, Nazi scientist Heinrich Zemo (father to Helmut Zemo). The of the Battalion had been mostly eliminated after Heinrich Zemo had murdered the original Citizen V, as the Nazis had hunted them down. The surviving (including Destroyer, Iron Cross, and Silver Scorpion) had reformed some years following the war to hunt down Nazi war criminals. V-Battalion was in years following the war hijacked by Baron Zemo, who had been killed by Scourge, but his mind transferred to the comatose body of John Watkins III (who at the time was the current Citizen V). Unbeknownst to anyone at the time, Zemo was using Watkins' body to further his own personal aims, using the Citizen V persona, and the V Battalion, to assassinate enemies of Zemo --- including, presumably, the parents of Tony Stark.
The Republic Oil and Natural Gas company were the direct competitors of Stark Industries for decades. Founded in 1932, the company grew into a sizable corporation by the time Tony Stark was born. Rebranding as Roxxon Energy Corporation following the death of founder J.T. Jones, the company had supplied both Allied and Hydra forces during World War II, and was one of the early funders of SHIELD. Hugh Jones, J.T.'s son, and successor to head the company, had used Roxxon for several illicit activities over the decades, running afoul of Earth's superheroes, and the United States government as well. Roxxon Energy Company has long been suspected of assassinating the Starks --- its direct competitor --- and staging the deaths as a car accident.
There is ample evidence for all three suspects to have been responsible for the deaths of the elder Starks, but never a definitive answer. The impact of their loss --- and the repercussions of their decisions and tactics as parents --- has affected nearly every corner of the Marvel Comics Universe. Since remain one of the driving factors to Tony Stark's rise, and mission, as the Invincible Iron Man.
