Amazing list, well done everyone involved and @hyruleguardian for sharing!
Some missing ones that come to mind out of the top of my head:
- English (and other non-Japanese) VS set cards (EDIT: @thymeee beat me to it while I was adding all the links to this post )
- Ishihara & Pikachu GX tag team
- Solid golden 20th anniversary Pikachu
- Japanese unlimited edition E1 set / decks
- Sample cards (i.e. Matchprint; FPO; double-bordered ones; the five press conferences Sample sets; etc.)
- Eevee, Pachirisu, and Croagunk Rumble set cards (EDIT: Ah, I now see @melchior had already mentioned these on the previous page)
- This unreleased Wailmer promo
- German Birthday Pikachu (I’m still trying to determine its origin, but I’ve heard multiple rumors it was a tournament promo with around 30 copies; definitely less than 1k though).
- Chinese POP cards
- Thai Jirachi 2019 trophy
- Inverted WB stamp promos (not sure if you want to include misprints/errors)
- Japanese unlimited edition L1, L2, L3, World Champions Pack are all so extremely hard to find that I doubt any card is printed more than 250 times, let alone 1,000…
- 016/DPt-P Pikachu promo (not sure how many were printed, so might be slightly above the 1k threshold, although I doubt it - EDIT: Also already mentioned before by @pieterpie, along with the golden 20th anniversary Base Pikachu… I really should learn to read… )
- 045/DPt-P Cresselia and 046/DPt-P Darkrai (a.f.a.i.k. no actual pictures has ever been seen, but there were some rumors 10 players had the points fast enough to receive the DPt-P versions before they switched over to the L-P versions)
- This 1st edition Japanese Feraligatr deck blister of which most got destroyed in a fire (mentioned by @shizzlemetimbers )
- Korean The Masked Royal promo (30 copies)
- Korean Mewtwo GX (36 regular and 17 Hyper Rare copies)
Non-TCG:
- Teach/Tryout set cards
- Groundbreakers TFG cards (still waiting for that article, @funmonkey54 )
I can name a few others I highly assume have less than 1k copies, like the German and Spanish Flying and Surfing Pikachu cards which I’m both still missing and have only seen once each, but I can’t say for sure how many copies were printed, and 1k seems a bit low for a regular promo.
I’ll see if I can find some more missing later on.
Greetz,
Quuador