Oh, boy, there are lots of these. Like most everyone here, I didn't get Chapel and Ambassador at first. Why would I want to trash without benefit unless Curses are around? Sure I can pass opponents this Estate from my hand, but that's all of my action, and what's more is I'm giving them points and taking points away from me!
Torturer and Minion were two other cards I had no idea how to use until I had spent some time on Isotropic: this is probably because they require multiple plays to unlock their full potential, and I started out as basically just a BM + X player. Watching those two chains beat me down regularly in the early days was more than anything the impetus I needed to start exploring more complicated (and more fun) chains.
Masquerade, yeah. Back in the pre-Isotropic days, I was all like "the drawing power of Moat and a pass that doesn't matter? For three? Why would I ever buy this?" Then it started to dawn on me that, hey, the trashing is useful too, and then I started to win a bunch with Masq-BM, and that's right about the time that Council Room stats came online and showed us all that, whoa, this is a sneaky powerful card.
Those are the most egregious examples, and I'm far from unique in all of them. But even after I started to become a good player there were things I misjudged. I thought Vault and Venture were horrible when they first came out; it took recognizing Vault's power to even think about ever buying Secret Chamber and I still don't think Venture is that good, actually. I expected Jester to be amazing and Remake to be weak, taking away the best part of Upgrade (the fact it's a cantrip), but by the time Cornucopia came out I had enough experience to correct these misapprehensions pretty quick: a couple games in and I knew Jester was a mild annoyance and Remake was instead an awesomer Steward. With Hinterlands, I underestimated JoaT for sure, and I knew IGG was good but didn't get how game-warping the IGG-Duchy rush was until I saw it in action.
Really, I've misjudged most of the cards at least a little bit one way or another. Probably the only card where I was right on the money from day one is Menagerie. I thought it was pants-wettingly powerful the second I saw it, almost always worth bending your play to make it work, and yeah it sure as hell is.