Compiled this list. A lot of small varieties got lumped together, mainly in Flygon's case (Since its not always clear if its deckout or with Champ or Weavile), some varieties were clear enough to get their own header. This is Masters Only:
Flygon (22 top, 12 win)
Gengar (11 Top, 6 Win)
Gyarados (11 top, 3 win)
Beedrill (10 top, 0 win)
BlazeRay (9 top, 0 win)
Kingdra (7 top, 2 win)
LuxApe (6 top, 1 win)
GeChamp (5 top, 2 win)
Palkia G (5 top, 1 win)
Machamp (4 top, 1 win)
Garchomp (4 top, 0 win)
Blaziken (3 top, 0 win)
GG (2 top, 2 win)
Luxray/Manectric (2 top, 1 win)
Dialga/Palkia/Luxray (2 top, 1 win)
SP Toolbox (2 top, 0 win)
Tyranitar (2 top, 0 win)
Dusknoir (2 top, 0 win)
AMU (1 top, 1 win)
DialgaG/Garchomp C (1 top, 1 win)
Mamoswine (1 top, 1 win)
Hippowdon (1 top, 1 win)
Empoleon (1 top, 1 win)
Charizard G (1 top, 0 win)
Abomasnow (1 top, 0 win)
Rayquaza (1 top, 0 win)
Abomasnow (1 top, 0 win)
Luxray (1 top, 0 win)
Porygon-Z (1 top, 0 win)
Leafeon/Torterra (1 top, 0 win)
Kingdra/Gengar (1 top, 0 win)
Lucario/Exploud/Gengar (1 top, 0 win)
Skymin/Venusaur (1 top, 0 win)
Luxray/Garchomp (1 top, 0 win)
Luxray/Gallade/Dialga (1 top, 0 win)
Blastoise/Garchomp (1 top, 0 win)
Uxie/Crobat (1 top, 0 win)
Toxitank (1 top, 0 win)
Rhyperior (1 top, 0 win)
Gallade/Raichu (1 top, 0 win)