I know the story of the HMS Glow worm and also about the German pilot that escorted a severely damaged B-17 to safety. However, did the Japanese did anything as gracious to allied forces during the war? I know they didn't follow the same ideology as Europeans and had a radically different doctrine of warfare, but did any Japanese individual or group perform any actions similar to the stories stated above?
There were several instances of Japanese forces "being nice" in WW2, although the practice, was, if not highly discouraged, not a common one within the Japanese military. One of the most well-known cases was the Japanese destroyer Ikazuchi rescuing some 400+ Allied sailors in the aftermath of the Battle of the Java Sea. The captain of the destroyer unilaterally made the decision to do so, despite the fact that his destroyer, which had a crew component of only around 219 men, would be extremely overburdened and vulnerable to enemy attack-not to mention outnumbered by survivors. While some of these survivors died or were otherwise mistreated in Japanese POW camps, the rescue was significant enough that a survivor (who became a British diplomat) went to Japan after the war to personally thank the captain. The captain was the only Japanese survivor of the incident, as the Ikazuchi was later sunk with all hands, and the captain had been reassigned to a different ship.
There were also individual instances of kindness by individual Japanese soldiers and civilians. One US POW recalled humming an old opera tune, resulting in an eavesdropping Japanese guard reminiscing and occasionally smuggling him food and malaria medication despite risking capital punishment. Several POWs who were "lucky" enough to be brought to Japan also occasionally benefited from civilians, whom for the most part still had positive opinions of America in general (caused at least partly by the largess of the US Navy in the wake of the Great Kanto Earthquake).
Of course, these instances were rare and were definitely not Japanese policy. While the official Japanese policy for POWs was that they be treated fairly, the fact that the Japanese military had terrible logistics and a poor chain-of-command meant that more often than not local officers had the call on who lived or who died. At least one Japanese general (who was, ironically enough, executed for war crimes) was relieved of his position for being too nice to the Filipinos after stopping his colonel from executing some Filipino leaders.