The links have pages with them listed. Note: some of these do not have lists.
Dark/Shining Pokemon: Dark; Sometimes Dark type instead/in addition to its regular typing, Shining; are shiny :P
Light Pokemon: Have more HP and supportive moves.
Pokemon ☆: Have different names and are shiny, can only have 1 in your deck.
Baby Pokemon: Can evolve into their Basic counterparts.
Crystal Pokemon: Colorless Cards that use 3 energy types and all have Poke-Bodys that change their type.
Delta Species Pokemon: Dual-typed and/or often a different type than normal (RSE era only)
Pokemon ex: Draw 2 prize cards from getting knocked out. (RSE era only)
Pokemon LV. X: Can use moves of the Pokemon it evolved from, Have more moves, abilities, and HP. (D/P/Pt era only)
Pokemon with held items: Appeared throughout D/P/Pt sets, worked similarly to Ancient traits.
Pokemon Prime: Cool looking card, is slightly more powerful than an average one would be. (HG/SS era only)
Pokemon LEGEND 2 cards that had to be played with their other half card; often had daul weaknesses/resistances/Types. (HGSS Era only)
Ace Spec: (can only have 1 in your deck)
Pokemon EX/M EX: (Get 2 prize cards for knocking out; M EX also end your turn upon evolving, unless you hold a spirit link)
BREAK Pokemon: Cards that give a Pokemon more HP as well as another attack/ability. Count as their own evolution stage.
Ancient Trait Pokemon: Pokemon with supportive battle traits, like abilities, but cannot be suppressed in the same way. (ORAS sets only)
Steam Siege Shiny Pokemon: Dual typed and shiny. Only appeared in the Steam Siege expansion.
Pokemon GX: Like EX, but have a GX move (you can only use 1 GX move per battle) and some evolve off of previous stages.
Prism Star Cards: You can only have 1 copy of each in your deck, and the card goes into the lost zone after being discarded.
Team/Trainer owned Pokemon: usually have effects trigger according to its owner and specific cards.
Pokemon SP: Have different names and are similar to trainers Pokemon.
Arceus Cards From the Arceus expansion: You can have as many of them as you would like in your deck.
Edit: I got a few I missed, Remembered Arceus.
Hope I helped!