The German Kriegsmarine kept up an active R&D division both before and during WWII. Many of their projects were canceled, only reached the prototype stage, or came to limited fruition. Bismarck and Tirpitz were the only vessels of their class completed. The giant H-39 battleships conceived as a follow on design were canceled. The German aircraft carrier Graf Zeppelin was only partially completed before the project was shelved. Her compliment of Fi-167 torpedo bombers reached the prototype stage but with no carrier to fly off of were canceled. The last great R&D drive of the Kriegsmarine was the Type 21 U-boat. Only four examples were completed in time to carry out war patrols but they would form the basis of later NATO and Soviet designs.

Arguably the most successful, and definitely most secret weapon created by Kriegsmarine R&D however was the Type 7 LS U-boat. These were a series of regular type 7 U-boat which traded most of their torpedo capacity for additional battery banks to improve their underwater endurance. Beginning in mid-1942 they were employed in one of the most daring operations of the entire war, Maritime Kampagne Eisdrachen (Maritime Campaign Ice Dragon).

Maritime Kampagne Eisdrachen was an attempt to render the increasingly small North Atlantic Gap deadly to allied shipping again. Allied Maritime air power was constantly extending its reach into the gap and conventional U-boat operations were increasingly dangerous. Maritime Kampagne Eisdrachen used the new long range U-boat in a brilliant plan to even the odds. The Eisdrachen boats would deploy in the Arctic where they would use explosive charges to cut loose icebergs which would strike Allied shipping. Even unsuccessful icebergs were a hazard to Allied logistics, costing valuable days as the convoys were forced to sail around them.

The icebergs proved a deadly hazard to allied shipping. Many of the small, slow, prewar ships could neither withstand nor avoid the newly floating ice sheets. Even the much larger liberty ships were not immune. The SS Carl Thusgaard which foundered in 1943 and the SS J. Pinckney Henderson which was badly damaged in a collision off the coast of Newfoundland are among the ships now believed to have been lost as a result of Maritime Kampagne Eisdrachen. The last casualties of the war not tied to unexploded bombs or mines are also believed to have been victims of an iceberg strike. Three sailors drowned aboard the SS Charles S. Haight when she was wrecked of the coast of Cape Ann in 1946.

Karl Dönitz secrecy precautions were so effective Maritime Kampagne Eisdrachen was only discovered after the war when allied analysts were going through the files recovered from the German navy compound. The Type 7 LS only ever sailed under hand delivered orders. No radio transmissions were ever made to the submarines during a mission. To avoid detection of their construction the submarines used off the shelf batteries from other U-boats. For their explosives they used the reliable 88 × 571 mm. R shell modified enroute with a timed detonator. Dönitz believed, correctly, that a small number of missing 88 shells would go unnoticed. To make their escape from France the Eisdrachen boats used a daring technique to escape detection. Once submerged the U-boats made the English Channel dash under battery power where they knew the English patrolled relentlessly with surface ships. By doing so they avoided the growing specter of long range Atlantic airpower.

To avoid the discovery of their mission even if the U-boats were spotted the Eisdrachen submariners used a two pronged stratagem. One half of the boats planted their modified shells on the underside of the ice sheets with divers in canvas diving suits. Although they had to work fast because of the limited supply of oxygen available to them from the submarine’s tether they were very effective. A half dozen shells could easily blow loose a 300 meter iceberg. The other half deployed teams to the surface who disguised their actions as the deployment of weather monitoring stations such as this one. Even when the stations were discovered by the Allies their true purpose was disguised.

I’ve posted some background sources here but the full story of Maritime Kampagne Eisdrachen only appears in Axis blockade runners of World War II by Martin Hubert Brice. His interviews with the survivors of the tense run through the English Channel are amazing. It’s a semi-rare book but I highly recommend it if you can find a copy.

MASSIVE EDIT: Ladies and Gentlemen this post is a joke. I hope you have enjoyed it as much as I enjoyed writing it. Maritime Kampagne Eisdrachen is unfortunately a complete fabrication. The ships, people, and books listed are completely real though. If you get a chance to read it Axis blockade runners of World War II by Martin Hubert Brice is a fascinanting book with several tales of great daring-do. Nazi Icebergs however appear no where in it.

EDIT: APRIL FOOLS IS FUN SOMETIMES, EH? :)

There was one rather unusual one being studied by SS doctors at Auschwitz, called Project 240, which the US Army jokingly dubbed "Operation Reefer Madness."

Suggested by Josef Mengele, the idea was to bomb London with bombs containing highly concentrated cannaboids in liquid form, followed by a wave of paratroopers who would seize key locations throughout the city, while the population was under the effects marijuana. Needless to say, this never got beyond basic testing, but it shows the extent that the Nazis were willing to go.

All the documents on Project 240 are currently on file at the Fort Lewis Museum on Joint Base Lewis-McChord, near Tacoma, where they were taken in 1945, as part of a larger transfer of medical documents which were examined by doctors from the University of Washington, in conjunction with the US Army Medical Corps. I found them while looking for serial number records of WWI era 1903 Springfield rifles, in hopes of creating a database of which rifles were issued to whom.

Sarin gas Nerve agents! I remember this one from my physiology class (I'm not a historian, but an engineer in training). Sarin gas is the first nerve agent. Nerve agents work by breaking down acetylcholinease acetylcholinesterase, which is the enzyme that degrades acetylcholine, the neurotransmitter, leading to a build up of acetylcholine. Now acetylcholine excites muscles, so when there's too much of it, the muscles will contract, and essentially freeze the person and they die by asphyxiation. EDIT: these are just some of the effects of sarin, /u/o-o-o-o does a much better job than me describing the biology.

Fun fact! Lack of acetylcholine is associated with Alzheimer's disease, which means that you can help combat the effects of Alzheimer's by giving a form of nerve gas. Check out the CDC's website for more facts about Sarin gas

The effects of Sarin gas nerve agents were accidentally discover by Dr. Gerhard Schrader in 1936, before World War II. Originally, it was intended to kill insects - which it was very good at - but when a little bit of the gas got out, the scientists in Germany learned of its effects on humans. They realized the gas' potential to kill and brought it to the attention of the War ministry. The gas was known as tabun, and after some research, the German government developed weaponized forms of this nerve agent, one of which is Sarin gas. It wasn't until 1945 that they were able to mass produce Sarin. Now here's where it gets interesting: Hitler wanted to deploy this gas onto allies, but a certain scientist persuaded him otherwise.

Speer, who was strongly opposed to the introduction of tabun, flew Otto Ambros, I.G.'s authority on poison gas as well as synthetic rubber, to the meeting. Hitler asked Ambros, "What is the other side doing about poison gas?" Ambros explained that the enemy, because of its greater access to ethylene, probably had a greater capacity to produce mustard gas than Germany did. Hitler interrupted to explain that he was not referring to traditional poison gases: "I understand that the countries with petroleum are in a position to make more [mustard gas], but Germany has a special gas, tabun. In this we have a monopoly in Germany." He specifically wanted to know whether the enemy had access to such a gas and what it was doing in this area. To Hitler's disappointment Ambros replied, "I have justified reasons to assume that tabun, too, is known abroad. I know that tabun was publicized as early as 1902, that Sarin was patented and that these substances appeared in patents. (...) Ambros was informing Hitler of an extraordinary fact about one of Germany's most secret weapons. The essential nature of tabun and sarin had already been disclosed in the technical journals as far back as 1902 and I.G. had patented both products in 1937 and 1938. Ambros then warned Hitler that if Germany used tabun, it must face the possibility that the Allies could produce this gas in much larger quantities. Upon receiving this discouraging report, Hitler abruptly left the meeting. The nerve gases would not be used, for the time being at least, although they would continue to be produced and tested. — Joseph Borkin, The Crime and Punishment of IG Farben

Basically, Hitler was told, that if Germany has discovered it, the Allies have discovered it as well and could produce more of it. So if he bombed the Allies with this, the Allies would bomb them back in turn. However it turns out that the Allies had no idea of it's existence until after the war. After the Allies discovered Sarin, they began to research it in order to develop and weaponize it based on the German specification. Even 30 years after it's discovery, Sarin was still one of the most volatile and deadliest poisons in the world.

Sources

Chemical and Biological Warfare Agents

The Third Reich at War by Richard J. Evans

EDIT: tabun = non-weaponized, Sarin = weaponized. Both are nerve agents, but there is a difference in the chemical structure and therefore deadliness of the two.

Weather Station Kurt was built by Nazis off the coast of Labrador (now part of Canada) in 1943 and found (Wikipedia says "rediscovered") in the late 1970s. Not exactly a secret program, but an interesting secret base of sorts. Source: Canadian War Museum exhibit

Edited typo, should have been 1943 not 1953. Stupid fat fingers.

Can a learned person here say whether Allies knew about this rediculous Monster, and if they were concerned by it?

The Schriever-Habermohl Project and the Nazi Bell. Either they were discovered after the war, or at the end but information on them was withheld, or someone here can kindly debunk the myth behind the development of Haunebu, Bell, and Vril disk shaped craft.

The V3 program, successor of the V2 and V1 went undescovered for a long time, and was destroyed at the end of the war.

Here's the wikipedia link http://en.wikipedia.org/wiki/V-3_cannon