I'm actually working on Ganondorf customs now. I want that sword move
His best move. I tried the custom moves against neobelmont and another friend.
So, for side specials 3 Dark chain works okay, but to a point, so 2 dark wave is the best. His normal side b is also could for its own kinds of combos.
Any Up Special is better than his normal up special, just a matter of preference. Both recover better, one better than the other.
Standing special Warlock Blade is still the best with its nice reach, speed, and super armor. Warlock Thrust on the other hand is actually pretty good...but the problem is it doesn't kill. Really easy to land though.
down special - It's a matter of preference and also match up and how you use the move. I feel 3 Wizard's Assault is the best. But if you think you can land 2 Wizard's Drop Kick without always putting yourself off the stage against Lucina, maybe use it against projectiles or to get distance, and then lead up to a combo, that move would be the best. It is actually possible to recover from it with how fast it is, in trade for the weaker damage it does for range and speed.