Ah, I had to re-read your post, since I was about to post some promos and Japanese cards. But I now see you’re asking for specific categories like the favorite single Holofoil Rare of all the Base Set through Neo Destiny sets combined.
Jungle set Jolteon. It was the second Holofoil I pulled as a kid, and I love the artwork on it.
Neo Revelations Shining Gyarados. The only Shiny Pokémon I pulled as a kid was Magikarp, so I was doubting to choose that one. But the artwork of the Gyarados is just so amazing I can’t choose any other. I’m not that big of a fan of the Shining Pokémon from Neo Destiny, apart from the fact that they have triple-stars, which I always thought was cool. But I agree the Shining Steelix is indeed great.
A tie between Expedition Base Set Kingler and Skyridge Magneton. Always loved both of those artworks and Pokémon!
This one is tough. In terms of artwork I like the Celebi the most, but the Kabutops and Charizard are both amazing as well, and I pulled the Kingdra as a kid, so that one is special to me as well.
A tie between the EX Ruby & Sapphire Electabuzz and Mewtwo. Both great artwork, poses, colors, and backgrounds.
5b. (missing category: EX era Holofoil Rares) Team Aqua’s Sharpedo. Always loved the blue and black colors of both the duo-type card as well as the artwork.
Charizard Gold Star. Although I don’t collect Charizards, its artwork just sticks out above the other Gold Stars imho, although all of them are amazing.
Cresselia LV.X. Hard to pick just one, but I like this one the most out of them.
7b. (missing category: DP era Holofoil Rares) This one was pretty tough as well, because none stood out largely above the rest. So I go with Myterious Treasures Celebi.
I’ll go with Unleashed Crobat.
A tie between the Undaunted Rayquaza and Deoxys LEGEND and Triumphant Darkrai & Cresselia LEGEND
9b. (missing category: HGSS Holofoil Rares) Undaunted Scizor. I like the pose and artwork as a whole.
Groudon SL
Black & White Reshiram for sure, with Zekrom being a close second
I’ll go with Plasma Storm Articuno EX, although I like Legendary Treasures Chandelu EX and both Meloetta EX as well
Plasma Storm Articuno EX again, with Next Destinies Zakrom EX and Dragon Exalted Rayquaza EX close behind