My precious… 
According to bulbapedia based on the distribution at regional tournaments, an estimated 189 of the 2003-2004 print, and an estimated 162 of the 2005-2006 (with Pikachu) print exist.
These cards were awarded to the top three competitors from each age division in the regional Japanese Battle Road Spring and Autumn Battle road tournaments.
It really depends on the definition of rare. I have several pop 1 cards, they are rare because of how difficult they are to grade like the Breakpoint League Cards…
Or because no one grades them, like this Cosmos Foil Blister Exclusive Greninja;
There is also rarity by distribution, which I think my Charizard Mega Battle Greninja probably is my rarest one.
Maybe not the rarest but my lowest pop card is this Shopping Pika Promo, only 61 PSA 10’s and 114 PSA 9’s so it a hard 10 to get. Only released to Pokemon Center shoppers in Japan from August 16-29, 2010. Love the art and the fact that I bought it from THE Ebirdman himself!
That’s the best phone card out there!
It’s probably nowhere near as rare as most of the other cards mentioned by others, but hey, they’re my rarest: 1st ed neo holo lugia, and a neo shining charizard.
A deck playtest card from a neo deck is probably my rarest card that ive come across. Besides that, a no-holo error dark dragonite that i pulled myself.
If we’re talking print quantity, this is probably my rarest.
If we’re talking conditional rarity/pop, these would be the rarest. Pop 3 and 2 respectively lol.
gold star celebi. nothing too crazy but still pretty freaking rare in the grand scheme of things. its not like people have hoards of crystal guardians boxes sitting around
While I have some lower pop Pichu Design Contest cards, I wanna say this 2005 Tropical Tidal Wave is my rarest card.
Population 5 in PSA10 but to the best of my knowledge the other 4 are all (or most?) in the diamond hands of a single asian collector. Would love to know if anyone on e4 has one of the others.
In terms of print numbers, I have a couple of lottery promos in high grades that I consider pretty rare. The Suicune is probably my favorite!
Don’t really have any cards that are very rare. Best guess is the Team Rocket Special Case cards. Anyone want to speculate how many of these there are? 2,500? Maybe 5000? Or more?
Could also be this phone card, but I don’t know its distribution numbers either.
Or possibly this phone card. I’m not sure if this is even an official Pokemon phone card or not, but I bought it about two years ago and haven’t seen another.
This is my rarest card, which I recently acquired. A heavily damaged Base Set disco test print.
Some members may recognise it - it has been through a few hands over the years. Its provenance is somewhat documented. Different kids in the Twin Cities metropolitan area somehow acquired a few of these in the late 1990s(?). A fascinating story, which I’d like to delve into further.
Whilst I have nothing against the ones which appeared in auctions over the past year (I was tempted to buy), I find the ones which were cut from a sheet, without the intention to sell as a collectible, more interesting.
Whoa I’ve never seen that last one before but the art does look remarkably similar to art from the pre-2000. Does the back resemble a typical phone card?
As for the Lugia/Hooh. I believe that came from collecting stamps for a Famitsu game magazine. Don’t remember specifics but I think I read it somewhere this past year?
