How I think some of the ghosts in Danny Phantom died, with evidence towards my theories.
Ember McLain: Died in a fire. She goes by the name "Ember" and her hair is literally made of fire.
Klemper: Hypothermia. He has ice powers, but is wearing clothes that are NOT suited for the cold.
Sidney Poindexter: Murder. A lot of people theorize that Sidney committed suicide, but I'd argue that that doesn't make sense for him- we see on Tucker's PDA that Sidney attended Casper High for four full school years, meaning that Sidney was only a few months away from graduation when he died (which would have been some time inbetween January 1958 and June 1958). It would be unlikely (but not impossible) for him to commit suicide so close to graduation. Also, Sidney's very angry and vengeance-focused. He has an intense hatred for bullies. He saw Danny play a prank and got so angry he started exploding stuff in rooms that he wasn't in. This would make a lot of sense for the ghost of a murder victim. Sidney is a classic vengeful ghost, except the people he wants vengeance on aren't around, so he takes it out on anyone who acts similarly.
Johnny and Kitty: Motorcycle crash. They're always together, so they probably died together; and Johnny has a ghostly motorcycle. Also, a motorcycle crash would be very bad luck.