Here's the ones that I can think of offhand:
Feast: Added +1 Action.
Scout: Added +1 Card and reduced the deck inspection to 3 cards (so basically, the first card's free).
Masquerade & Throne Room: I was applying the 2e versions before 2e made them official.
Tribute: Made it discard the bottom card of the player to your left and the player to your right (in 2p, your opponent is both to your left and your right and so discards the bottom two cards). This wasn't really for balance purposes so much as to make it feel like less of a "single-target attack" (it's not, but tell that to someone who keeps getting good cards discarded; it was either make this change or have the card vetoed entirely).
Scrying Pool: Removed the attack (but kept the self-spying). It speeds things up, and the card's plenty powerful without the attack.
Pearl Diver: Added the option of discarding the revealed card so you don't get stuck repeatedly revealing the same Province.
Smugglers: Let it copy any opponent, not just the player to your right. This was because of a game where two experienced players both went for a strategy where winning the split of a certain 5-cost card was crucial, and the third, less-experienced player, messed around with cards that weren't that helpful. Needless to say, the mirror player on the left won the split by a large margin due to Smuggling from the other mirror player, leading to the realization that the next time this situation happened, we'd know that whoever sat to the left of the newbie would be at a disadvantage, and no one would want to sit there. Letting it copy everyone means that no one's stuck with an inferior Smuggling target.
Black Market: Replaced the Black Market deck with 5 Events; each Black Market gives you a Buy that can only be spent on one of those Events (and all of those Events are available for every Black Market play). This was designed primarily to ease setup/cleanup (so I didn't have to keep fishing single cards out of my binders), but also serves to remove a lot of the weirdness associated with Black Market (i.e., random selections with potential unfairness where one player gets access to a vital card and the others don't; it also eliminates playing Treasures and buying stuff in the Action phase, which wasn't really a problem IMO, but it does simplify things to avoid it).
Walled Village: Changed the below-line text to "At the start of Clean-up, you may spend an Action to put this onto your deck." Since it's a card I paid for specifically, I wanted it to actually be relevant.
Boons in general: I replaced the random deck with a semi-randomly generated "Boon map" that you maneuver around, removing the unpredictability and potential unfairness. I also tweaked Sacred Grove (Boons that provide money are no longer excluded, since we use markers to track it anyway) and Druid (can now grant any Boon without moving around the map; we don't even use the map if Druid is the only Fate card) to fit the new system.