There was definitely some collaboration between the two, though the vast distances between the two countries certainly didn't make it easy and hampered how much of it there could be. To speak in my particular area, the naval aspect of the war, I think one of the more interesting aspects of this came in the form of the Yanagi Missions. These were a series of operations carried out by Japanese submarines, which covertly transported valuable resources, designs, machinery, personnel, etc. to Germany, and returned to Japan with reciprocal amounts of German cargo. Some similar operations were carried out by German submarines going to Japan, but these have no direct relation to the Yanagi Missions. To go into more detail about each one:

I-30: Codenamed "Sakura," on 2 August 1942 she arrived in Lorient carrying a cargo of 3,300 lbs of mica and 1,452 pounds of shellac, and the blueprints for the Type 91 aerial torpedo (I-30's own Type 95 torpedoes were replaced with older Type 89s for the mission, Japan didn't want Germany to get those secrets yet). Her arrival came with much fanfare and celebration, the crew met Hitler in Berlin and even visited Paris. During her stay, I-30 was examined by Kriegsmarine engineers and fitted with a Metox radar detector and her Type 96 AA guns were replaced with a quad Flak 38. She departed on 22 August, leaving her Yokosuka E14Y1 floatplane as a gift and carryingblueprints for the Würzburg air defense ground radar and a working set, 5 G7a aerial torpedoes and 3 G7e electric torpedoes, 5 torpedo data computers, 240 Bolde sonar countermeasure rounds, rocket and glider bombs, anti-tank guns, a Zeiss AA fire control system, 200 20mm AA guns, one million Yen worth of industrial diamonds, and 50 Enigma machines. On her return trip, she struck a mine off Singapore and sunk, with most of her cargo being lost.

I-8: Codenamed "Flieder," on 31 August 1943 she arrived at Brest carrying tons of tungsten, rubber, tin, quinine, and medicinal opium, a full additional crew to take command of U-1224 (a U-boat to be transferred into Japanese service in early 1944), plans for the Type-95 torpedo, a reconnaissance aircraft, and submarine equipment. Prior to that she met up with U-161, who transfers 3 crewmen and installs a FuMB 9 Wanze radar detector on her. Again after much fanfare, she departed carrying an E-boat engine, radar and sonar equipment, quad 20mm AA guns, bombsights, electric torpedoes, naval chronometers, penicillin, and several military and civilian personnel. After a rather perilous journey, she arrived back at Kure on 21 December.

I-34: Codenamed "Momi," on 11 November 1943 she departed Singapore carrying tons of tin, tungsten, raw rubber, and opium. Allied codebreakers intercepted communications regarding her mission, and she was torpedoed and sunk by HMS Taurus on 13 November 1943.

I-29: On 5 April 1943 she departed Penang carrying 1 Type 89 and 2 Type 2 torpedoes, 2 tons of gold bars, blueprints of the aircraft carrier Akagi, a Type A midget submarine, and several passengers. On 26 April, she meets U-180 in the Mozambique channel, carrying blueprints of a Type IXC/40 submarine, a sample of a hollow charge, a quinine sample, a torpedo tube containing a gun barrel and ammunition, 432 Bold sonar decoys, documents for the German emassy in Tokyo, and several important Indian revolutionaries. The two transfer cargo over the following day, and then return to their bases. I-29, codename "Matsu," departs for her Yanagi mission on 16 December 1943, carrying 80 tons of raw rubber, 50 tons of tin, 2 tons of zinc, 3 tons of quinine, opium, coffee, plans for obliquely-firing cannons, and 16 passengers. She also had I-8's German radar detector refitted onto her. She arrived in Lorient on 11 March 1944, fanfare ensues, they also meet Hitler and visit Paris. Some of her AA guns are replaced with German guns. She depared 16 April with a HWK 509A-1 rocket motor, a Jumo 004B engine, drawings for an Isotta-Fraschini torpedo boat engine, a V-1 buzz bomb fuselage, TMC acoustic mines, plans for a glider bomb and radar equipment, bauxite, mercury-radium amalgam, and 18 passengers. I-29 was sunk in the Luzon strait by USS Sawfish on 26 July after her communications were intercepted, losing most of her cargo.

I-52: Codnamed "Ginmatsu," departed Singapore on 23 April 1944 carrying 120 tons of tin, 102 tons of tungsten, 54 tons of raw rubber, 9.8 tons of molybdenum, 11 tons of tungsten, 3.3 tons of quinine, 2.88 tons of opium, 2 tons of gold, 58 kg of caffeine, and 14 passengers. On 22 June she meets up with U-530 off the Cape Verde Islands, where some crew and cargo exchanges are made before the two go their seperate ways. En route to Lorient, I-52 was sunk by two torpedoes dropped by aircraft from USS Bogue, and some of her cargo was later found by the carrier's destroyer escorts. She would be the last Japanese submarine to attempt a Yanagi mission.

And as mentioned previously Germany did attempt several reciprocal voyages, but none were successful except for the transferral of U-551 into Japanese service as Ro-500 in 1943. Those aside, the Germans did have assistance from Japanese subs in patrolling the Indian Ocean and German commerce raiders did operate in the Pacific Theater.