Danny's evil older self from The Ultimate Enemy is only addressed in-universe as Phantom and listed in the credits as Dark Danny. That hasn't stopped the fandom from almost universally calling him Dan. The Tie-in Game Boy Advance with the same name outright calls him Dan Phantom, which doesn't help his case. Maybe the writer was a fan?
College Trio: Collective name to refer to Vlad, Jack, and Maddie.
CW: Because sometimes "Clockwork" is just too long to bother with.
GW: Because sometimes "Ghost Writer" is just too long to bother with. (And his initials are written on the pediment of his mansion.)
Frightmare: Nocturne's temporary name prior to the episode "Frightmare" airing.
Jack Plasmius: Halfa Jack in "Masters Of All Time".
Master of Longwinded Introductions: Technus.
The Magnificent Nine: The first 9 episodes of Season 1.
Halfa: The only character to use the word "halfa" (as in, "half a kid, half a ghost") was Sidney Poindexter, a student who died in The '50s and is therefore stuck using fifties mannerisms and speech patterns. But it's not like the show writers ever came up with any other name for the concept, and "half human and half ghost" doesn't exactly roll off the tongue, so the fandom has decided that "halfa" is as good a word as any.