Super Mario World
Mario and Luigi cause the extinction of all dinosaurs.As you can see from the map, Dinosaur Land just vaguely resembles Earth. Taking the Pangaea theory into account, the different continents may actually be underdeveloped modern continents. So, when Mario and Luigi save the princess and defeat Bowser, they inadvertently cause the extinction of the dinosaurs.
King Koopa was killed off for real.Adding to the example from the cartoon above, Mario and Luigi in "A Little Learning" rig the lava pipe to have it flow into Koopa's bedroom. The episode itself ends Koopa screaming on his bed with the lava building up around him. The next episode, "Mama Luigi," happened to be the Super Mario World series finale and the last animated episode of the Mario Bros. franchise to date. Koopa was referred to by Luigi and only appeared at the end of his flashback, adding to the suspicion that the Mario Bros. carried out the dirty deed.
Peach suffers from a mental disorder and is getting treatment.Taken from a Cracked user but, Mario and Luigi fixe pipes in a mental institution and are recruited by the staff(the toads) to handle Peach's problematic ex-boyfriend(Bowser), who cannot get over the fact he is bad for the person he loves and is slowing her therapy. All the bizarre imagery is how Peach views these events in her disordered mind. Super Mario World was a request by the staff to the plumber to take Peach on vacation, believing some time away would be helpful. Unfortunately Bowser found out where they were going. Sometimes Bowser is not so bad in Peach's delusions because despite his problems he was good enough to date once and he defends her honor against worse guys people in her life, like Smithy and Grodus. The go-kart, sport and party games are instances where Bowser is better behaved, if only slightly.