Pokemon MD Red Rescue Team and Blue Rescue Team use Gen 3 Movesets.
Pokemon MD Explorers of Time, Darkness and Sky use Gen 4 Movesets.
Pokemon MD Gates to Infinity uses Gen 5 (same as Gen 6) Movesets.
Pokemon Super MD uses same Gem 6 Movesets.
Thanks to GameFaqs Movesets for Pokemon Super MD and Serebii Spin-off Dex for the rest.