I'm going to answer this looking at the RN's midget submarines, and so this answer cannot be generalised to Japanese, Italian or German midget submarine operations.

The RN operated three main classes of midget submarines during the war. The first was the X-Class, which came in three series - two prototypes, X3 and X4, the original X5 series of six boats, and six improved boats of the X20 series. A modified version of the X20s was used for training as the XT-class, with 18 built. The final class was the XE-Class, which had modifications to improve habitability, stealthiness and reliability in the tropical conditions of the Pacific Theatre. Eighteen were ordered, but only eleven would be delivered before the end of the war. There were also the post-war Stickleback or X51 class of four boats, designed for training and to deliver nuclear weapons to Soviet harbours in the Baltic. All of these classes were operated in a very similar way. The operational boats had a four-man crew, with one officer as a commander, one as a navigator, an engine-room artificer to manage the engines, and a diver (though sometimes two divers were carried). Divers were not carried in the two prototype boats or the XT craft.

The X-craft were short-ranged vessels, capable of travelling just 80-90 nautical miles submerged without recharging on the surface. As a result, they were often towed to the vicinity of their targets by a larger submarine. When this was done, two crews were carried. The first, the passage crew, would man the X-Craft while it was under tow, keeping it steady, stable and connected to the towing submarine. Once the vicinity of the target was reached, the passage crew would transfer to the towing submarine, and be replaced by the operational crew which would carry out the attack. To attack a target, the various X-Craft carried two two-ton charges. They were positioned on either side of the boat's circular hull, and hence were known as 'side cargoes'. The craft would manoeuvre its way under its target, release the charges, and withdraw to a safe distance. The submarines could also carry limpet mines, deployed by the diver. Once the weapons had been released, the midget sub would withdraw and return to its rendezvous with the towing submarine. Missions would typically last only a few days. The X-craft had few amenities for the crew. There was a single bunk between the four men, placed forward above the batteries. This was, apparently, an unpleasant place to sleep thanks to the risk of getting a shock if you moved too much, and those who slept there often suffered headaches caused by the hydrogen gas produced by the batteries. For cooking, there was just a hotplate with a cooking pot. Most meals were composed of whatever tins came to hand, emptied into the pot, stirred to mix, and given the appetising name of 'potmess'. The boats had a single toilet, located in the 'Wet and Dry Compartment' (the airlock for the diver). This was cramped and complex, and, like all submarine toilets, had a constant risk of 'getting one's own back', or having the pressure outside the submarine blow the contents of the toilet back onto the user.

The X-Craft made four main attacks on Axis targets following their entry to service in late 1942. The first attack was Operation Source, an attack on heavy units of the German fleet in the Altafjord in Norway. Six midget submarines, X5-X10, were allocated to this attack, towed from the UK by six conventional submarines. Three of the midgets were to attack the battleship Tirpitz, two more would attack the large cruiser Scharnhorst, and the last was to attack the 'pocket battleship' Lutzow. The first two midgets and their towing submarines departed their base at Loch Cairnbairn, Scotland, at 4pm on the 11th September 1943. Three more would sail at two hour intervals after this, but the last midget/tower pair did not depart until 1pm on the 12th. The first few days of the passage were uneventful, but on the 15th, X8 slipped her tow rope and was lost by the towing submarine due to a confused helm order. Fortunately, she would run into X7 and her towing submarine. X9 was not so fortunate. Her tow rope parted during the early hours of the 16th, and she was lost with the whole of her passage crew. On the 17th, X8 had stability problems, as both of her side cargoes were starting to flood. When the second of these was jettisoned, it exploded, damaging the midget and forcing her to be scuttled. On the 18th, X7s operational crew came aboard, but due to bad weather, the crews of the other three surviving boats waited til the next day. The X-craft left the towing subs in the evening of the 20th.

The midgets spent the night of the 20th crossing the outer German mine barrier on the surface. When daylight came, they dived, making their way to the Bratholme islands, where they would charge their batteries for the final run-in. Early on the morning of the 22nd, they made their attack, leaving the islands shortly after midnight. X6 and X7 successfully penetrated the Kafjord where Tirpitz was anchored, dodging German mines, nets and patrols. X6's periscope flooded, and she would accidentally run aground, damaging her gyro compass. Without these, she could not effectively navigate. Even so, her commander managed to get close alongside Tirpitz's bow, deploying her charges, but he was forced to surface the boat to fix his position. Spotted and brought under a heavy fire, he scuttled his boat and brought his crew off with no casualties. X7 had no navigational problems, and correctly deployed her charges. Unfortunately, while withdrawing, she ran into anti-submarine nets. While surfacing to try to make her way over the top of them, she was fired upon. The damage made the submarine impossible to control. Her commander chose to surface, in the hope of getting his crew off. However, after the first man made it off the boat, she sank. One more man escaped the boat after it sank, using breathing apparatus, but the remaining two men would not survive. X5's fate is unknown. She likely made it into the Kafjord, and was sunk by the Germans, though it is unclear whether or not she deployed her charges. She was lost with all hands. The last boat, X10, was to attack Scharnhorst. When attempting to enter the Kafjord, her gyrocompass stopped working. Her back-up magnetic compass also failed, and shortly afterwards, the motor for raising her periscope caught fire. She remained in the Altafjord until sundown, hearing the explosions of X6's and X7's charges. Believing the attack to have generally been successful, she withdrew. She met up with one of the towing submarines on the 28th, but the weather made it impossible to take the crew off until the 29th. X10 was towed back across the North Sea, but the expectation of worsening weather and problems with the towing rope meant that she had to be scuttled on the 3rd October. Operation Source was a qualified success. While all the midgets had been lost, along with one towing crew, six men from the operational crews dead and six captured, serious damage had been done to Tirpitz, rendering her unusable.

Of the remaining three attacks, only one was similarly exciting. In 1944, X24 made two attacks on a floating dock in Bergen harbour, Norway. In both cases, she was towed across the North Sea by the submarine Sceptre. The first attack, Operation Guidance, took place in April. X24 successfully penetrated the defences of the harbour, and laid her mines before withdrawing and rendezvousing with Sceptre. Unfortunately, the charges had been laid under the merchant ship Barenfels, rather than the dock. Barenfels was destroyed, but the dock, the main target of the attack survived. On the 11th September, X24 returned to Bergen to carry out Operation Heckle. This time, the charges were deployed in the right place, and the dock was sunk. X24 would also survive this operation. In February 1945, six XE-craft were sent to the Far East, along with the submarine tender Bonaventure. These submarines made one attack on Japanese forces, Operation Struggle. This targeted Japanese cruisers based at Singapore. Two midgets, XE1 and XE3, departed Bonaventure in Brunei Bay on the 26th July 1945, towed by Spark and Stygian respectively. On the 30th, they were released off the Horsburgh Lighthouse, at the eastern end of the Singapore Strait. XE3 made it to her target, the cruiser Takao, with little trouble. Unfortunately, Takao was lying in shallow water, greatly complicating the task of attacking her. Even so, limpet mines were attached to her hull and the side cargoes deployed under it, though in the process of doing so, XE3 was nearly caught underneath her. Meanwhile, XE1 was attempting to attack the Myoko, moored further along the strait than Takao. However, she was held up by heavy Japanese patrols, to the point where she would be unable to attack Myoko and escape before XE3's charges exploded. Instead, her commander chose to attack Takao, dropping his charges near her hull and withdrawing. The explosions sank Takao, but, as she was in shallow water, her upperworks remained above water.