Nah Jim Moriarty > Charles Augustus Magnussen.
Though I did like how Charles had a mind palace, as well.
Yeh he was a very good villain, and his mind palace was awesome. But Moriarty man, Moriarty is on a different league of awesomness.
The difference between Moriarty and Magnussen is quite clear.
Moriarty = Consulting Criminal
Magnussen = Businessman
Moriarty = Criminal Mastermind
Magnussen = Napoleon of Blackmail
Moriarty = Unnecessary Evil
Magnussen = Necessary Evil
Moriarty = Sherlock's Rival and Equal of Sherlock
Magnussen = Mycroft's Rival and Slightly above Sherlock
Ofc Moriarty will have more fans, he had 2 whole seasons and also the "comeback" whilst Magnussen had just one episode.