Boaty McBoatface-- The reason we're all here. The British Natural Environment Research Council thought they would get a name like Shackleton, Endeavour, or Falcon for their new 200 million GBP polar research ship. The internet decided it should be 'Boaty McBoatface' instead. Unfortunately, the will of the people will not stand, as the UK's Science Minister (and noted killjoy) Jo Johnson has said that they will be looking for another name among the submissions.
Vulcan And Romulus--When it came time to name two moons of Pluto, many people, including William Shatner (Captain Kirk) thought that at least one moon should be named Vulcan, after the alien world in Star Trek. Their case was bolstered by the fact that Vulcan is the name of a Roman god, and many celestial bodies are named after mythological characters. Unfortunately, the IAU disagreed with the majority, and named the two moons Kerberos and Styx instead.
COLBERT--Stephen Colbert handily won the competition to name a node of the International Space Station after, who else? Himself. NASA rejected the will of Colbert nation, naming the node 'Tranquility' after the site of the first crewed moon landing. As a consolation prize, the treadmill in Tranquility was named the Combined Operational Load Bearing External Resistance Treadmill, aka, the COLBERT.
Mr. Splashy Pants--There is actually a whale splashing around in the ocean somewhere named Mr. Splashy Pants. When Greenpeace held a naming competition back in 2007 for a humpback whale that they were tracking, the winner by far was Mr. Splashy Pants, with 78 percent of the vote. Unlike NASA, the IAU, and the NERC, Greenpeace decided to listen to the people, and embraced the name.