Well, one significant difference in methodology was that German scientists conducted tortuous human experiments on unwilling prisoners in the concentration camp system.

Much is said about Josef Mengele, but he was far from the only participant--there was an entire scientific community built up around the concentration camp system. These experiments were generally justified in the minds of the authorities because they would save German lives down the road.

Some examples follow.

1. Freezing: Prisoners were forced to lie in freezing cold water until they passed out from hypothermia, at which point they would either be allowed to die--and then autopsied--or various attempts were made to revive them. This was an attempt to find ways to revive hypothermic sailors or airmen fished out of the sea. All the normal things you'd imagine were tried, but Himmler himself ordered--and watched--a trial where women were forced to attempt to have sex with a prisoner to see if that would revive him.

2. Altitude sickness: Prisoners were forced into barometric chambers, and then subjected to changes in the interior pressure to simulate bailing out of an airplane at various altitudes.

3. Phosgene: Prisoners were exposed to phosgene gas, a deadly gas used as a chemical weapon in WWI. The experiments were purportedly to attempt to develop better protections against the gas. The prisoners were cynically called "volunteers" when SS officials questioned their deaths during a later investigations.

4. Anti-bacterials--Prisoners were given very deep cuts--one woman describes a cut to her thigh that exposed her thighbone--then deliberately infected with gangrene-causing bacteria so that german doctors could determine the effects of various potential anti-biotic compounds.

I really wish that this was all, or that these were even the worst experiments conducted. Unfortunately, you can read about even more terrible experiments in Nikolaus Wachsmann's KL: A history of the Nazi Concentration Camps. As far as I've ever heard/read, neither the US nor UK conducted human experimentation on such a widespread scale, nor with such disregard for the safety of the test subjects.

The Germans were weapons makers and engineers, the Allied nations, especially the USA and USSR, were industrialists.

Germany put a lot of effort into innovative industrial processes- such as making synthetic fuel, and welding armour plating- and weapons design in the sense of making the best weapon.

Their tanks- that is the major types used in the war as opposed to their early war efforts intended mainly for peacetime training- were very well laid out with powerful engines, large turrets to accommodate big guns (and with scope for improvement), with every feature well thought out including radios, optical sights, crew access and so on. The same went for their aircraft: they quickly did away with biplanes and their machines had not just powerful engines but fuel injection, many automatic systems to manage settings that had to be changed with altitude, and really well designed guns that were reliable and took up little space.

They were also prepared to make seemingly anything: half-tracked motorcycles, adaptors to start a tank in the Russian winter by hitching it up to a Volkswagen, special units to blow hot air into plane engines for the same purpose, a special automatic rifle just for paratroops, a specialised night fighter plane, a 200-tonne tank, the Maus. In a stereotypically Germanic way, they put design effort into everything: even their fuel storage can was so perfect the Allies simply copied it and we use it today as the 'jerrycan'. And of course their expensive programs in rocketry, jets and advanced submarines.

All this came at a price. Firstly, German civilians got nothing, consumer goods were always hard to come by and the German standard of living dropped. Food was usually hard to come by, as agriculture was hardly mechanised. Secondly, the love of advanced weapons meant the Germans never made enough mundane things like trucks and boots. But the real problem the Germans had was they could never make enough, they were always tempted by quality and innovation over quantity. Although they were good at managing production lines, and had to get really good as they decentralised their industries, their production numbers were always far too short in crucial areas, especially tanks.

In comparison, the Allies were not so militarily obsessed and their business ethic, and the USA and USSR were not so far apart in the sense that they both loved factories and production numbers, saw them focus on producing vast quantities of weapons that only had to be 'good enough'. Business-trained individuals tended to have a lot of political power (Lord Beaverbrook managed British aircraft production, in the US large corporations were contracted to manage government-owned mega factories). They also had a very good understanding of their economies and optimum use of resources, thanks to Keynesian economists who worked out how to measure these things. Roosevelt appointed John Kenneth Galbraith to manage the US money supply and prevent inflation, which he did with great skill. The German economy was actually chaos.

In terms of technology, in Germany it was down to the Nazi regime picking favourites. The British were more ad hoc, but were fortunate to have strong leadership in jet engines, which was supported to a sufficient extent, though not enthusiastically, and radar. They shared all their technology with the USA, which was two years behind in entering the war so they also benefitted greatly from British battlefield experience. Having a more 'civilianised' research sector, as well as a much larger, better-resourced one, the Allies were often able to produce more useful and applicable innovations. Examples would include their code-breaking operations, the Mulberry Harbours used in Normandy, subtle use of convoys to avoid U-boats, clear 'bubble' canopies on aeroplanes, better battlefield medicine and food distribution, mass-produced Liberty ships and miniature escort aircraft carriers.

The Soviets were always pretty good at the basics, and simply sought to copy and develop innovations from elsewhere to fill out the secondary considerations. Production there had the typical Stalinist characteristics, and a struggling factory manager could be executed as readily as a disgraced general. The Soviets had obstacles like no other country, having to move factories in late 1941, and re-start them with totally untrained labour. They lacked key resources and had limited skills in chemical production, metallurgy and so on, as their entire industrial economy was really only a couple of decades old.