Here is the list of Pokemon that's available on the server but not included in the base Cobblemon mod.

CindyMons (made by Spirit-Cindy)

Tyranitar, Arceus, Deoxys, Deoxys-Attack, Deoxys-Defense, Deoxys-Speed, Diancie, Ferrothorn, Latias, Latios, Mega Beedrill, Mega Blastoise, Mega Blaziken, Mega Diancie, Mega Gallade, Mega Gardevoir, Mega Gengar, Mega Latias, Mega Latios, Mega Lucario, Mega Metagross, Mega Mewtwo-X, Mega Mewtwo-Y, Mega Salamence, Mega Swampert, Miraidon, Regice, Regigigas, Regirock, Registeel, Sneasler, Iron Moth, Iron Thorns,

Fakemon

Mysticara, Mysticara-Angel, Mysticara-Fallen, Armored Mewtwo, Iron Champ, Mega Machamp, Shadow Lugia

Fakemon (Pokemon Xenoverse)

Gengar-X, Tyranitar-X, Mega Weavile

GabenMons (made by The Gaben)

Keldeo, Koraidon, Sneasel, Chien-Pao, Iron Bundle, Scream Tail, Terrakion, Virizion, Cobalion

SaltMons (made by Salt-Kitchen)

Slowpoke, Slowbro, Slowking, Heatran, Kingambit, Kyurem, Meltan, Melmetal, Rotom, Rotom-Fan, Rotom-Heat, Rotom-Frost, Rotom-Mow, Rotom-Wash, Hisuian Samurott, Landorus-Therian, Mega Lopunny, Mega Mawile

Allone's Additions

Axew, Fraxure, Haxorus, Trapinch, Vibrava, Flygon, Houndour, Houndoom, Nymble, Lokix

MoreMons

Dewpider, Araquanid, Heracross, Capsakid, Scovillain, Dreepy, Drakloak, Dragapult, Iron Valiant, Larvesta, Volcarona, Croagunk, Toxicroak, Drilbur, Excadrill, Annihilape, Absolutely humongous 14x14 blocks Guzzlord