I make Pokémon-specific lists for collectors pretty often, and sometimes they request to include cards featuring the specific Pokémon in the artwork. I usually go over this list first, and then also look over my own collection sometimes:
These cards above have loads of other Pokémon in their artworks in particular (@shizzlemetimbers Blaine’s Quiz cards are also in this list 
).
Even then you’d sometimes still have to search on some artworks. Especially in the Jumbo cards, or cards with 15+ Pokémon in them like the illustration contest ones. Here two examples:
Another thing that comes to mind for this thread are some cards I’ve included in my National Index collection.
To give some examples: did you know that male Magikarps have yellow whiskers and female Magikarps have white whiskers? That means the Base Set artwork is a female Magikarp. Likewise, the Vending Machine series Dodrio is a male (black necks), whereas all other Dodrio artworks are females (beige necks):
Some more examples:
Arbok has three different patterns available on TCG artworks:
Some artworks of Magneton (like the Fossil Magneton) has one of the Magnemites upside down:
And I could give loads and loads of other examples:
- Gym Heroes & Gym Challenge Charmanders both have a horn on their back (this one I learned from @smpratte Scott’s binder video)
- Mantine’s fish isn’t a mini Remoraid in some artworks
- Some Exeggcute artworks are missing the sixth egg
- The Magnemite artworks sometimes have the blue/red magnets reversed in comparison to other artworks
- The Team Rocket Ekans has stripes around its body, instead of only its belly
- etc. etc.
Please take a look at my National Index collection for all these kind of variations!! And if you know any missing, let me know. 
Greetz,
Quuador