Yeah, the Leon reaction command at Hollow Bastion in KH2 is one of the most recent surprises I've seen.
Other than that, there's the fact that if you cast Firaga on Riku-Ansem during the fight at Hollow Bastion in KH1, he'll retaliate with Dark Firaga, which he never does otherwise. And then there's the exploding rock in Destiny Islands that covers the mushroom and self-destructs if you somehow get stuck on it. Also, that there's a hidden cutscene when you finish your first visit to Traverse Town where if you go back and find the Dalmatians' House, Leon will be there and he'll explain more about the puppies.
KHReCoM has a really interesting one: There are two secret cards that you can unlock that aren't listed on the game's database, a Gold Card and a Platinum Card. I forget what the Gold Card does, but the Platinum one makes you invincible, which is OP.
For KH2, there's a lot I didn't know about it until I was older. One thing I didn't know was that you can actually fight Shan-Yu's falcon. Or that there's a rare reaction command during the Sark/MCP fight where you can climb a wall and instakill Sark with a headshot. I also never even knew about the Struggle tournament toward the end of the game until I was older, not that I missed out on much with that (though it was amusing to hand Setzer's pompous ass to him Keyblade-master style).
There's some other stuff from BBS and DDD that I didn't learn about until I was older, too, but those basically just boil down to gameplay mechanics that I never bothered to experiment with. In terms of neat little oddities, KH1 and 2 (though mostly 1) take the cake.