Toon Disney (ended 2006)
In the animated version of W.i.t.c.h. its Nerissa, becasue she is a devious individual and uses all kind of trickery to achieve her goals, plus she's much more powerful than Prince Phobos.
In the comics I pick Prince Phobos, a major reason why is that he's more mysterious, for example he doesn't make a full appearance until #7, and he does more stuff like turn Aldarr's children into flowers,and Caleb back into a flower, and also he's crazy in #5 its revealed he destroyed all of his statues when assuming the throne. In the Endarno saga he establishes himself as the #1 W.i.t.c.h. villain. Plus, he has a great name for a villain "Phobos" which is Greek for fear. Prince Phobos is basically the iconic arch-villain of W.i.t.c.h. just like Lex Luthor is for Superman, The Green Goblin for Spider-Man and Dr. Doom for the Fantastic Four.