It was named such because it was 42nd on a list of revolutionary ideas from the brain trust of Tony Stark, Reed Richards and Hank Pym. During the Civil War, all super-powered beings whom failed to register with the government where taken captive and transported to this prison inside the Negative Zone.
During the Civil War, many of the heroes who where captured managed to free themselves and return to earth. After the Civil War the complex was mostly abandoned until Blastaar took control of the building during the "War of Kings" crossover, making it his new headquarters. Sometime later he even managed to capture X-man Cyclops and Hope inside his complex, although these where later freed thanks to Steve Rogers (Captain America), some X-men and Namor.
Trivia: The Complex was also known under the name of "Negative Zone Prison Alpha", "Wonderland" and "Fantasy Island".