I'd say that the B-29 qualified as a "superweapon", it flew higher and further than any bomber up until that point, and carried more ordnance. The bombing campaign of the Home Islands would have been a very different beast indeed without it, and the program cost more than the Manhattan Project($3 Billion to $2billion).
Stuart Slade, probably the only outed nuclear targeter on the Internet, really likes to tout the B-36 as the ultimate non-nuclear "superweapon" to come out of WW2. Work began on it before Pearl Harbor because of a requirement to being able to bomb Europe from North America, it was shunted aside/slowed down in favor of the more conservative B-29 when it was obvious the British Isles weren't going to fall. When it finally entered service it was the highest flying, longest range, and heaviest(in terms of ordnance carried) heavy bomber in history up until that point. It still had a bigger bombload than it's successor(the B-52).
EDIT:I realize that "nuclear targeteer" is one of those things that is hard to back up, for obvious reasons. So, I'd like to adjust it and say "Stuart Slade, defense analyst and consultant(and occasional published author, shitty self-published novels notwithstanding) really likes to tout the B-36 as the ultimate non-nuclear superweapon to come out of WW2".
While not as glamorous as the B29 or the A-bomb, the development of the radio proximity fuse for artillery was every bit as groundbreaking & hush-hush. AAA was surprisingly inefficient in WW2 (something like 1500-2000 shells for every plane shot down) with one dramatic example being the US 8th AF raid on Hamburg by 720 bombers in mostly overcast skies suffered just one aircraft lost to flak. The German defenses had consisted of 44 heavy flak batteries that fired a total of 24, 416 rounds. With the advent of the radio "VT-Fuse" that could detect when it was close to a target, this dropped to around 200-300 shells per plane.
They were mainly used in areas where there was no danger of an unexploded shell being recovered by the enemy and reverse engineered. Two roles they contributed greatly in were the protection of naval ships from Kamikazes, and defending Britain against V-1 attacks. It was also capable of being used for air-bursts on ground targets, a definite game changer.
Yes, bats! There was a transportation system in development to bring bats from America and release them over Japan. The bats had small incendiary devices on them that would blow up after a set time.
The idea was the bats would hide among the largely wooden structures of Japan. So when their bomb went off, it would create a very large fire quickly.
Tests were going good. They found a great way to cool the bats down during flight so they'd be docile, but aware enough to resume flying when the plane was over Japan.
Despite great testing, funding was pulled. The leaders of the project had no idea why, but it was because the military got another way to ignite an entire city, the nuke.
Source: fantastic documentary on history channel back in its world war 2 days. I can get more sources if it's required.
EDIT: Here's the wikipedia entry that gives some more info, and an article by The Atlantic discussing the Bat Bomb too.
The are two answers to this question, and since I am a historian and we can get away with being self-contradictory in the name of making a point, I will give you both of them.
The first answer is to say, "no." Nothing else under active short-term development by the United States really qualifies as a "superweapon" — a weapon that was seen as a true "game-changer" in its own right, that was talked about in exceedingly hushed tones at the highest levels, that was considered to have deep implications for future international diplomacy. President Roosevelt demanded exceptional, unusual secrecy regarding the atomic bomb; General Groves applied counter-intelligence measures to its production that were remarked upon as unprecedented in scale by his contemporaries; the amount of resources commandeered for its development was practically unthinkable (around 600,000 Americans worked on some facet of the bomb's development, ~1% of the entire civilian labor force); the Secretary of War wrote about it in code in his diaries (and he did this with no other weapon); the Presidents (both Roosevelt and Truman) conferred about it repeatedly with other Allied leaders (e.g. Churchill, later, briefly, Stalin); and so on. There is no other wartime development that goes into this category, that deserves the title of "superweapon" as opposed to just "new, high-tech weapon."
The second answer is to say, "yes." The atomic bomb was one of many new developments during the war where academic science, military resources, and industrial production were combined to produce technologies that would have definitive wartime outcomes. The B-29 bomber cost more than the atomic bomb to develop and produce, the MIT Rad Lab produced new radar technologies that helped the US and UK dominate the air and sea, and weapons like the proximity fuze proved vital for both theaters of the war. These weapons are in some sense superficially more humble than the atomic bomb — they are smaller, had less secrecy surrounding them, and did not lend themselves to lofty pronouncements — but they did provide decisive advantages to the Allies because they had them and the Germans and Japanese did not (or at least not to the degree that the Allies did).
Since I don't have to choose which of these answers I like the best, and can offer them both up simultaneously, I will. There are elements to each that ring true, but you need the sum total of both perspectives to properly contextualize what the atomic bomb meant as a "superweapon." It had extraordinary elements, but it had elements that were not as unusual as one might think, once one sees the whole context. The real "superweapon" of World War II was the coordination of science, military, and industry, because it enabled the development of all other "superweapons." It was something that the United States did not really have in World War I, and was not a "natural" thing to do by any means. It took direct interventions by scientists to make happen, notably Vannevar Bush of the Office of Scientific Research and Development, who had a personal connection to President Roosevelt that facilitated all of this coordination. It also laid a template for how weapon development would continue into the Cold War, evolving into the so-called Military-Industrial-Academic Complex.
Well, kind of. In addition to the explosive capabilities of nuclear weapons, the energy creation and powering of machinery was considered as well. My grandfather worked on a project to develop a nuclear powered aircraft. They also developed the nuclear powered submarine at the same time. Not sure if they qualify as super weapons, but they definitely were not intended to be passenger planes. More information about this particular project can be found here.
I think the Norden Bombsight qualifies. While certainly not as flashy or sci-fi as the atom bomb, radar, or even the B-29, it had a high level of security and secrecy (From what I read, and gather from my grandfather, who was a small part of security for it).
It probably was not a game-changer like the atom bomb, or even radar, but absolutely part of the technological evolution of war that made WW2 so interesting.
believe it or not there was something that people carry around with them that was classified top-secret. Albumin, a protein that floats around in your bloodstream was discovered to be an effective way to prevent shock in injured troops. it provided a much need boost to survival rates. I read about in it Douglas Starr's nonfiction book "Blood" (they begin talking about it on page 104) it's really an interesting part of the book.
While not a weapon itself, the first computer, ENIAC was for military use. It was commissioned in 1943, though not finished until after the war, in 1946.
There was a guy came up with the idea of using bats to bomb the Japanese with. The military eventually spend 2 million developing bombing system for the use of bats. They planned to strap an incendiary device to thousands of bats, place them within small cubbyholes within boxes and then drop them over cities within Japan. The idea was that they would then fly and nest under the eves and roofs of the mostly wooden buildings in the Japanese cities. Then the timed incendiary device would go off thereby hopefully setting the buildings, cities on fire. When they tested the dropping of the bats they set a few of the base buildings on fire thus proving that it would work. http://www.theatlantic.com/technology/archive/2011/04/old-weird-tech-the-bat-bombs-of-world-war-ii/237267/