If I were Germany early in the war, say in 1942 then I use them to destroy Moscow, Leningrad and Stalingrad…if Russia is still fighting after that, use them against the remaining industrial cities in the East (Chelyabinsk, Magnitogorsk, etc.). In either case, the point is to decisively win in the East (where the vast majority of the German war effort was focused…). In 1943 or 1944 (after the tide of the war has turned) use them tactically such at the battle of Kursk to increase my defensive capacity, the idea being to bleed the Russians into capitulation. In 1945, the war is lost so hit London, Moscow, Leningrad, Stalingrad, New York and Washington DC (via submarine) to try to bluff a negotiated peace.
If Russia, then Berlin and tactical use on the east front.
If Japan, then the American West coast cities (Los Angeles, Seattle, San Francisco) the Panama Canal, Pearl Harbor, and probably Sidney, Australia. For them, the war was against the USA and UK.
If the USA, then I would pretty much do what they did, unless I had the A-bomb earlier in the war in which case I would bomb the larger cities of Japan and Germany (Tokyo, Osaka, Berlin, etc.) instead of Hiroshima and tiny Nagasaki.
If Great Britain, I absolutely use them to destroy the U-boat pens and would probably bomb the larger cities and industrial areas of Germany with the remaining bombs.