Recently I started a very chill new collection goal to have fun at local events and to satisfy that urge I always had as a kid to gather the rarest, most unique and obscure Pokémons I could find (encountering a missingno in yellow blew my mind). I remember playing Gold back in the day and an npc at Lake of Rage mentioned seeing a pink Butterfree, so I made list of the few weird Pokémons I knew and I spent hours and hours searching for them in vain (not knowing how the game worked had it’s magic). So now I want to at least have 1 copy of each proto-Pokémon or significant variant printed (giant, color variant, different pattern, old designs, etc). Here is what I have so far, can also include 1996 carddass Pikachu, Charmander and Kabutops as their designs also changed and a non identified Pokemon is shown (Kabutop’s back). Any help is appreciated!
Are you only looking for non-TCG cards/oddities featured in the anime? Otherwise, off the top of my head, there are a few non-canonical arts of some Pokemon that exist in the TCG.
Blaine’s Charmander with the bump on it’s back (if I remember right, it was a prototype design for Charmander)
And the different Arbok pattern variants in the early TCG that don’t show up anywhere else, as far as I’m aware (a normal Arbok followed by two pattern variants).
I’ll add more if I remember anything else. Neat collection idea!
Edit: Another one that I remember another forum member pointing out: early Mews having colored feet (which is absent in his design today).
No, I’m looking for anything that can fit into a binder pocket. These examples you mentioned are exactly what I was talking about, thanks a lot! Hope the list keeps adding up! I also remember early Gyarados design with an extra fin coming out of it’s head (carddass, Giovanni’s).
There are some Sealdass cards that showcase the old colorings of Pokemon including bluish (Sugimori) Gengar (and Bulbasaur line), Wigglytuff without the later added pink shading, Charmander with blue rather than green eyes, the old coloring of Tauros, etc.
Japanese phone card, Oddish used to be black with colored leaves. Venusaur also used to have bamboo on its back. Bonus points for Gyarados being on this card 
There is some interesting variation with Hydreigon. Sugimori, front and back sprites (the BW back is a bit iffy but appears to suggest 7,) and most of the cards show 7 fuchsia-colored tufts of fur.
These however all feature 8 tufts:
A not so obscure variation it would seem, it’s even found in the anime:
This 8-version I would certainly describe as a rather unique variation because the bottom one mirrors the tallest vertical one on the top:
Thanks for the suggestions guys, I would have never thought about that Wiggly, great find! Ofc that 1998 phone card would be a dream to own. Seaking and Hydreigon that’s also something I would have never noticed!
Not sure if you want to include these but just in case, there are a few digit variations:
- Zapdos used to have 3 talons, now has 4
- Mr. Mime used to have 4 fingers, now has 5
- Raticate used to have 4 fingers, now has 3
- Aerodactyl used to have 4 fingers, now has 3
- Golem used to have 3 front toes and 4 fingers, now has 4 front toes and 3 fingers (Fossil is the obscurest one with 4 fingers + 4 front toes on the right foot only)
At the Pokemon Live musical they handed out MechaMew2 cards. FYI they are larger than standard cards
This is the kind of nuance that you would only ever find on e4. Nice eye! 
this is hilarious. I have never seen that before. This would have definitely scared the crap out of me as a kid
Ahaha this is a big discovery, thank you!
Right in the non-tcg
So was Giovanni the one that set us on the path of the future with the SV paradox Pokemon? 