Superman and John F Kennedy seem like a match made in heaven - handsome men who represented everything positive about America. That means it should come as no surprise that the two were friends, and that JFK once helped Superman keep his identity secret by posing as Clark Kent.
In Action Comics #309 Superman was scheduled to go on a This Is Your LIfe type TV show, but the producers wanted to have his pal Clark Kent on as well. That would be a problem, clearly, as Superman is Clark Kent, so Kal-El turned to the man he trusted the most. John F Kennedy, wearing a Clark Kent mask, appeared on TV to take suspicion off of Superman's secret identity. Yes, JFK knew Clark was Superman and yes, he had nothing better to do than to appear in disguise on a TV show.
The second time Kennedy and Superman teamed up it was in the service of physical fitness. Kennedy enlisted the Man of Steel to promote his Presidential Physical FItness program, intended to keep American youth in shape (he'd have shit his pants if he saw the kids of today).
The comic was created in partnership with the Kennedy administration, and it was scheduled to be printed in Superman #168... which went to press right when Kennedy was assassinated. The story was swapped out with something that was sitting a drawer and it looked like Superman's battle for physical fitness would never see the light of day.
But it ended up running just two issues later at the insistence of the Johnson administration, which felt it would be a fitting tribute to the fallen president. DC did as LBJ wished, but they were skittish about putting the dead president on the cover, so they went with "What If Luthor Was Superman's Father?":
This story has recently been back in the news; Al Plastino, the artist, donated his work to Jackie Kennedy, thinking it would end up in the JFK Presidential Library. He was recently shocked to discover the art had never made it to the Library, and that it was scheduled to be sold in a JFK-related auction today. He sued to stop it, saying the art must have been stolen. As of today Heritage Auctions has taken the art off the block.
By the way, that story where JFK dresses as Clark Kent? It hit newstands a week after Kennedy's assassination, too late to be actually pulled. It had a great cover, though: