Diamond & Pearl sets had the S subset spread out among the sets SH01 - SH12: SH1 - SH3, SH4 - SH6, SH7 - SH9, & SH10 - SH12
Rotom subset RT1 - RT6 in Rising Rivals
4 Alph Lithograph cards have their own card numbers
Call of Legends had the Shinings SL01 - SL 11
Skyridge has a Holo subset H01 - H32
Aquapolis had Holo subset H01 - H32 Legendary Collection, Expedition had Box Toppers
You could count the parallel foil set as a subset, "cracked" holo versions, non-holo and holo versions from theme decks.