I'm tied for these three.
KH1 (non-boss): Invisible.. because they're fucking beasts. The first time I fought them, I quickly found out how challenging of a fight just two of them can be, unless you're 60-70 and above, I think.
Wyverns.. because I have more than one favorite KH1 heartless. Along with Invisibles, I was upset these didn't make KH2's heartless roster. Seriously, where's mai blue Wyverns in the 1,000 heartless battle. I was somewhat okay with the lack of behemoths, but wyverns to? The thing I like most about them is they're generally annoying to fight with just the X button. You actually have to use magic and ranged attacks half the time or else, you'll probably fall and when you get back up there.. the heartless might be back, so you still can't activate the crystal thing.
Defenders - These guys are fucking awesome as well. I love deflecting their fire balls and nulling their freeze with fire. Oh, and another enemy where mashing X doesn't work as much as usual. Oh, and they're one of the few non-boss enemies that actually killed me. (I was kind of low leveled though and I was stuck with the stupid wooden sword when I fought it. I let Beast do most of the work, but somehow got killed anyways. He was the last one you had to fight before opening the entrance doors.)
KH1 boss - Darkside.. 'nough said. (Well, I had two+ line responses for the others at least.)
Actually, fuck him..
Kurt Ziza/ Phantom - even if the latter lacked attack variety, both were somewhat challenging, especially on Expert mode. Kurt Ziza even killed me four times on Expert mode... He never killed me on Normal mode. I couldn't believe I got owned the first time I fought him on Expert mode, despite being level 93. I think it was because I was being stupid with item usage though. I used them up too quickly because I was a bit overconfident.
KH2 - Umm.. Storm Rider and Shadow Stalker/ Black Thorn? Seriously, I can't think of many awesome KH2 heartless. Then again, I did kind of like the Graveyard. At least, them and the Toy Soldiers actually can kill you at low levels. I found most heartless in KH2 as easy, even at lower than normal levels. Crimson Jazz were somewhat hard at lower levels, but they were generally more annoying than hard.
Anyhow, I taking it you going to pin this, right?
Edit: I already posted in such a thread (which I think got moved to Favorites), but if we're going to have an official/ pinned thread, then I might as well post again.