In WW2, which midget submarine program was the most successful?

This is a rather long answer outlining the strengths and weaknesses of various nations' midget submarine fleets. If you just want the short answer, skip to the last paragraph. During World War II, the UK, Italy, Germany, and Japan had midget submarines. The US, the USSR, and China did not.

The Royal Navy had two main submarines. The X-class submarine was built from 1943-1944, eventually replaced by the XE-class submarine. 20 X-class submarines and at least twelve XE-class submarines were built. There were also a few unsuccessful submarines, such as the Sleeping Beauty and the Welman submarine. Six of the X-class were lost in battle and one in training. Another six of the X-class were training-only. The operational X-class were mainly used in preparatory work such as taking surveys of Normandy beach and cutting torpedo nets in harbors. However, six were used in Operation Source to neutralize German warships. All but two of the submarines involved were lost in this operation. XE-class submarines were used similarly. However, only four of them ever saw action. In 1945, they were used to cut Japanese telephone cables off the coast of Vietnam and China.

Italy had 16 midget submarines over the course of the war. There were two classes, the CA-class and the CB-class. Two CA-class subs were manufactured Between 1938 and 1939 and two more were manufactured in September 1943. They were originally designed for coast defence but later modified as attack craft. Italy planned for them to attack New York Harbor, but their transport submarine was sunk and the plan was scuttled.

Seventy two boats [CB-class] were ordered... but only 22 were laid down. 12 boats were completed before the Armistice.... [Six boats] fought the Soviets [in the black sea,] sinking two submarines.

Italy also had a few unsuccessful miniature sub designs.

Germany had four types of midget subs of which only one was successful. The first was the Biber.

The Biber was hastily developed to help meet the threat of an Allied invasion of Europe. This resulted in basic technical flaws that, combined with the inadequate training of their operators, meant they never posed a real threat to Allied shipping, despite 324 submarines being delivered. Wikipedia- Biber

Bibers took part in many missions, but few ever survived them. For example, in the first Biber operation, 14 took part. Only two even made it to the operational area. In 1944, the Bibers deployed against traffic going to Antwerp. In the first attack, 18 were sent out and one returned. They sank only one ship-- the Alan A. Dale. This was one of the the only ships ever sunk by a Biber. Further operations in the area lost over thirty more Bibers.

The Molch, another German Midget submarine, was highly unsuccessful. Although 393 were built, it suffered heavy losses.

The complicated system of tanks made it difficult to control during combat operations.... Due to the ineffectiveness of the Molch in combat operations, it was later used as a training vessel for more advanced midget submarines. Wikipedia- Molch

The Neger was a torpedo-carrying craft. Although not designed as a suicide weapon, the torpedo would often fail to release from the submarine when fired and would carry the craft with it to the target.

About 200 vessels of this type were manufactured in 1944.... However, the Neger turned out to be very hazardous for its crew, and up to 80% of the crews were killed. In return one cruiser, one destroyer, and three Catherine Class BAMS minesweepers were sunk in 1944 with the weapon.

Due to this, the Neger was eventually retired and withdrawn from service.

The last major type of German midget sub was the Seehund. It was the most successful of the German Midget Submarines. Of the 1000 planned, 285 were completed and only 35 of those were lost, mostly due to bad weather. However, it was designed in 1944 and only used in the last months of the war. It's small size made it difficult for it to be picked up by ASDIC. It was also a very quiet craft, making detection by hydrophone impossible. It mainly operated around the German Coast and the English Channel, attacking merchant ships. It sank nine and damaged three.

The Japanese had the largest fleet of submarines of any of the navies in the pacific although Germany had the most overall.

The Japanese navy also built submarines with the fastest underwater speeds of any nation's combat submarines. They employed 78 midget submarines capable of 18.5 to 19 knots submerged, and built 110 others capable of 16 knots. Japanese Submarines

These were by far faster than any other midget submarine sailing at the time. Few could go over 10 knots.

These were comprised of one main type- the Ko-hyoteki Class Submarine. It was subdivided into three types: A, C, and D. Five type A participated in the attack on Pearl Harbor, but only two made it into the harbor and none survived it. Three type A attacked Sydney Harbor in 1942, but one was sunk before it could do damage. The other two survived but sank before they could return to their transport submarines. They damaged only one ship however. Two type A's also took part in the Battle of Madagascar. One was lost at sea and the other seriously damaged one battle ship and sank an oil tanker. Type D's were mas produced-- even more than the type A's and type C's. 115 type D's were completed by the end of the war and almost five hundred more were under construction. The Ko-hyoteki also played a defensive role in the Aleutians and alsewhere in the Pacific.

To put a conclusion on this lengthy answer, I would say the Japanese had the best midget submarines. However, the Germans had the best program as the Japanese did not often utilize their fleet in important offenses.