A lot of people seem to be confused about Tony Stark's heart and the arc reactors he used to keep it beating. Here's a quick rundown.
The movies never came out and said it but the arc reactor is a cold-fusion reactor. It creates power by causing hydrogen atoms to combine into helium. The sun is a hot reactor. The extreme heat and pressure in the sun causes fusion. Cold fusion has been hotly debated for nearly 30 years after some scientists claimed to have produced cold fusion using palladium.
The movies never go into it in detail but Howard Stark either designed the large arc reactor that powered Stark Industries or at least did a lot of the initial design work on it. He also recognized the limitations of palladium and theorized a new element that would be superior to Palladium in creating cold fusion reactions. For some reason, the arc reactor was seen as a dead end. Possibly it cost too much to produce or was just to finicky to mass produce without the new element.
In Iron Man, Tony Stark is hit in the chest with shrapnel. The doctor on hand were not able to remove the shrapnel while working in caves in Afghanistan but he was able to create an electro-magnet that pulled the fragments away from Tony's heart. At first Tony had to carry a car battery around with him. Since Tony is an engineer and not a doctor, he created a small power source to power the electro-magnet. He treated it as not being a big deal but it was actually very difficult to reproduce. Once back in his lab, Tony was able to create a much more powerful arc reactor.
We never got any details but apparently any time the power to the electo-magnet was cut off, shrapnel started pressing on Tony's heart causing cardiac arrest. It never actually pierced Tony's heart or no amount of magnetism could fix it.
By the second movie Tony was having problems. Palladium was building up in his system and poisoning him. While the electro-magnet kept Tony alive, it also prevented treatment. If the electro-magnet was removed then Tony would go into cardiac arrest before the shrapnel could be removed.
Palladium isn't particularly toxic and the palladium in the arc reactors was contained. Possibly the reactor was vaporizing the palladium allowing it to be absorbed into Tony's body. That would explain why the reactors kept wearing out and why the technology was considered a dead end. Palladium is expensive so feeding a giant arc reactor would be expensive.
Anyway, Howard Stark couldn't have known that Tony would need an arc reactor to keep himself alive but he did leave clues for Tony on how to improve the arc reactor. All it needed was for technology to be so advanced that someone could build a particle accelerator in his basement.
So the Starks created a new (apparently unnamed) element and the arc reactor was stabilized without the toxic side-effects.
By the Avengers, Tony was apparently trying to market the new arc reactors. He bragged that he had a monopoly on clean power. In Avengers II, Stark was wearing a Hulk-killer armor powered by multiple arc reactors.
Then at the end of Iron Man III, Tony cured himself. It was a simple solution, actually. He built a large electo-magnet and had a surgeon operate under that. The large magnet kept the shrapnel away from Tony's heart long enough for a surgical team to extract it. This seems simple enough but for some reason it confused people. I've seen two different rants about it as a plot hole.
One last note - in the comic books Tony wore an entire chest plate that actually assisted his heart. It was battery powered and he was constantly charging it in the early years. His suit had extra batteries in the pods he wore on either side of his waist and they all fed into a unified system. If Tony's suit ran down then his heart stopped.
At one point Tony's heart condition deteriorated and he had to wear the entire suit of armor except for the helmet just to keep his heart going.
By the early 1970s, Tony got a heart transplant using artificial tissue. This was fine for a while but then Tony's body started rejecting the tissue and he had to wear the armor to assist his heart again for several years. Tony also converted his armor to run on solar power which was great unless he fought at night or in a deep hole (this actually happened). Eventually batteries got better and Tony stopped having monthly heart problems.
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