Glady, I am blessed with a good enough memory that it dates back to my starting days of Dominion. Now this was only a year ago (back when Alchemy was the newest expansion) and I'm only 26 so this isn't too hard. But I vividly remember some of the earliest games I played with friends and it was amazing. A sense of general awe came over me after that first game. I buy this card, shuffle and now it's in my hand? Wow!
Not surprisingly, this was the first deck building game I had ever played and buying and getting to play cards was such a revelation. It was a totally different game from all the Euro worker placement / cube gatherers we had played before and required quite a different mindset. With those Euro games, every cube was precious and we couldn't waste a single one of them.
So, obviously, there were a lot of cards in Dominion that I had no idea were so good until I started to learn more about the game, play on BSW, discuss on BGG and eventually move over to Isotropic and these forums.
Chapel comes to mind as the epitome of cards that I didn't understand at first. Trash money and victory points. Wait, what? I didn't understand tempo back then. How wrong I was. It's now my 2nd highest "Win Rate Given Avail" card and that's saying something. My "Win Rate With" is at 1.48 ± 0.14.
The Cursers I understood quite early, especially after having been cursed yourself you start seeing the value of giving your opponents both dead cards and negative VPs.
Torturer I actually picked up on later, because I somehow assumed it worked like Militia, never letting one get down to less than 3 cards. My jaw dropped to the floor the first time someone played multiple Torturers in a row.
Ambassador is also a card that I underrated in the beginning. Maybe that's because there's no bold text on the card. It looks so harmless and even gives free gifts.
I had problems with a lot of the Alchemy cards in the beginning, but I've grown fonder of them as time goes by.
Are there any cards that you remember misjudging horribly when you started playing or when expansions came out? Did you have a "Jack"-experience with some of the others? Tell us...