This is tough. In perusing this thread, I’ve come to the conclusion that most of the items in my collection that I consider “rare” aren’t actually rare and are just expensive because they’re widely desirable. Then again, I suppose that’s how I’d prefer it… I’ve always focused on set cards over promos and never been one for error cards, so that rules out most items in the hobby that are genuinely hard to find.
In terms of items that are “rare” in the sense that very few exist, I’d have to go with sealed stuff. I imagine my sealed Mysterious Treasures box is probably my rarest item in this regard. In general, I think pre-BW sealed boxes are among the scarcest things out there, although it’s clearly impossible to estimate an actual number.
EDIT: I have a PSA 10 Japanese Shaymin Lv.X 1st Ed, which appears to be a pop 6, so maybe that lol. Very few graded.
I should actually overwrite the last choice and say my Shinings are the rarest. This is because they have 3 stars meaning they have more rarity than the trophies that have two or other rares that this has the same amount as those do but with more.
A collector found this in his collection years ago and even posted on E4 and reddit, the masses thought it was fake, however I tried to buy it from him knowing it was real, I offered almost $600 USD which was a lot of money for a Pokémon card at the time, only to be told that someone has offered a little more - eveidently it was likely Tony lol. I fired back a higher offer but never heard back, likely because he had already sold it.
Tied between lugia (psa 3.5 also which I’ve never seen on another pokemon card not that it means much) and suicune /L-P lottery prizes both had 1k copies given away.