In terms of appearance and background, Pumpkaboo! I absolutely adore it and I love its role as a Pokemon that leads spirits to the afterlife.
In terms of gameplay, Giratina! My original Giratina from Pearl is my strongest Pokemon in a mainline game, ever. Its Ghost and Dragon types let it hit anything but Steel types for STAB neutral or better damage in its original game, and starting in Gen 6+ it can hit everything but the Wigglytuff, Kingambit, and Grimsnarl lines (and Azurill and Mega Audino) for STAB neutral damage. And it has 120 base Special Attack in its Origin Form and Calm Mind access.
(Both of these aren't just my favorite ghost-types, but my favorite Pokemon ever. Spooky Pokemon are my favorites.)