I primarily use those which make the game more accurate historically. The Allies are assigned two each. Germany and Japan receive three each. In all cases, some are automatically assigned.
For Russia, Lend-Lease, but not quite the way it is in the rules, and Non-Agression Treaty, as it is a more historical situation. For Lend-Lease, the Russian player rolls two dice, and receives that amount of Lend-Lease credits, which are then used to buy units. These National Advantages are assigned.
For Germany, Luftwaffe Dive Bombers may only be used if their are no fighters present. Historically, Stukas were easy prey for fighters if Germany did not have complete air superiority. Otherwise, whatever three that the German player rolls.
For the UK, Radar and Colonial Garrison are assigned.
For Japan, the Tokyo Express is assigned, and in place of Dug-In Defenders, I simply have all Japanese infantry taking two hits to kill, i.e. “Fight to the Last Man”. The player can make either one or two rolls, depending on whether he/she used the FLM rule.
For the US, Island Bases and Marines, sometimes raiding my A&A Pacific set for the units.
I also normally give the US the Combined Bombardment and Long-Range Aircraft technologies to start. Because of the size of the US, the US has always put a high emphasis on range in its aircraft, and was using external drop tanks and internal bomb bay tanks in its aircraft from the start of the war. The pre-war planning for an amphibious war in the Pacific had the US Navy thinking shore bombardment long before the war started.
If I used LHTR rules, I would allow the Japanese to use the Super Battleship advantage only if the US also gets the same rating for its Iowa-class ships. One change would be that the Yamato-class ships would defend against surface units at a 5, but need a 4 or less to defend against air attack. The Japanese naval AA fire was simply not that good throughout the entire war. The Iowas stay at 5 and 5, as the US had the best naval AA fire of the war.
For the US, I would still use the Island Bases, but also go with War Economy, however, production cost reduction would be 2 IPC and not 1. US wartime production was enormous.