My understanding, based on things I have read over the years, goes like this:
The Germans tried to keep actual combat units in the regular Army ("Wehrmacht") supplied with standard issue weapons, so they had priority for Lugers and P-38s. This broke down after the disasters of 1944 (the Falaise pocket in France and the "destruction of Army Group Center" in the East). After that, units got whatever was on hand, including 11mm Reichsrevolvers from before 1908.
The "private armies" of Hermann Goering and Heinrich Himmler got weapons from alternative sources. Paratroopers began to get FN High Powers after the fall of France. I have heard the SS got a lot of Radom P-35(p)'s, but I can't say I have seen photos to prove it.
Luftwaffe aircrew in bombers got Lugers at first (that is what the Krieghoff Luger contract was for) but they were replaced with 32 automatics after or during the Battle of Britain. I think Me-109 pilots may have had 32s from the start, because the 109 had a very cramped cockpit. I think the fighter pilot Heinz Knoke mentioned having a Mauser pistol at some point in his book "I Flew for the Fuehrer", but I don't remember what period of the war it was, and I don't think he said if it was a 1914 or an HSc.
Tank crewmen sometimes seem to have had 9mm pistols, and sometimes 32s. Tanks are also cramped, and I have read that tankers liked the Sauer 38H because it was both DA and hammerless.
I think rear area soldiers who were issued pistols (logistic units, rear area security, army flak, occupation troops, etc.) got a lot of the oddball or less desirable guns, like the FN 1922s, Hungarian P-37(h), the CZ 24, the Uniques, etc. In the Italian theater, they would get Berettas, at least after Italy surrendered in 1943. I've heard the occupation troops in Norway got the Norwegian 45s.
The Germans issued a LOT of pistols, as barnetmill says. I think this was because from 1939 until 1945, their troops were in countries where they were actively hated. Brutal reprisals kept the number of actual attacks low, but most troops would have felt safer with a gun, even when off-duty in quiet areas.
Just as a side note, nobody seems to know what was done with the pistols imported from Spain.
All the above, except for the part about Wehrmacht combat units, seems to be based on anecdotal evidence. I don't think the Germans were as well organized and systematic as people think they were. The spread of the war beyond Poland caught them by surprise, and after the first winter in Russia, they were always trying (and failing) to keep up with losses of equipment.