English only? 1st edition Base Set and Red Logo Pack Fossil/Jungle booster boxes, and maybe Skyridge as well somewhat.
Japanese included? Some unlimited edition sets that do have booster boxes. The World Champions Pack mentioned above comes to mind, but was only sold as 25-card booster packs and no booster boxes were available a.f.a.i.k. Unlimited E1 comes to mind as well, but we don’t know for sure where they come from. I’ve heard rumors it came from decks given at certain events, but there are some cards like Charizard and Alakazam that can’t be explained that way. I doubt there were any booster boxes for this set, though.
Maybe unlimited edition L2/L3 booster boxes? Or the No Rarity Base Set (where there booster boxes of these at all actually, @shizzlemetimbers )? And some Japanese booster boxes from the PCG era are also almost non-existent, as mentioned by @fourthstartcg in this quote:
All languages? 1st edition Spanish Neo Genesis is close to non-existent (even took me 4 years to find a Spanish 1st edition Pikachu for my own collection to give you an idea how rare the single cards already are). 1st edition Portuguese Jungle sets are pretty rare as well; Korean unlimited edition Base Set comes to mind of course; I can imagine the two Polish booster boxes aren’t too easy to come by either; Dutch unlimited edition Base Set booster boxes are pretty rare as well (1st edition not really on the other hand). And there are probably more examples.
Greetz,
Quuador