Alt-VP. Ignoring Gardens/Silk Roads/etc. can be safe enough in 2er if you can buy out the provinces before they can bloat their alt-VP up to more value than the provinces. In 3er, two players going for 3 pile can just hammer you while you have to down 12 provinces all by yourself (more than 50% harder than 2er). On the flip side, if you go gardens, the other guys only have to split the provinces 6:6 in order to end the game (giving you maybe 2/3rds of the time you'd have to bloat gardens in a normal game).
Bishop. You give your opponent a free trash. In 2er he can go do something else better than you and fly. In 3er, the other 2 players have to race each other AND you. Likewise, once you start bishoping VP, the other guys have to SPLIT any VP you don't gain so they can't push as long towards megaturns.
Council room, governor, embassy, etc. The relative advantage you get is lessoned because you are giving out advantages to two opponents. For instance, even though the extra card isn't likely to make the difference between province/not province in 2er. It is almost double in 3er (e.g. if there is a 20% chance of giving the opponent a province they otherwise can't get, in 3er that rises to 36% and up to 49.8% in 4er). Likewise, unlike in 2er you can keep compounding this advantages making it play really different (e.g. Moat becomes phenomenal if something like Council room/Border Village/Ghost Ship is out).
Another biggee is Masq. Discard/Masq becomes a LOT less useful as you only gimp one player by passing a copper & forcing them to pass something good (like silver). Masq/Possession gets a good bit safer. You also have a LOT more estates to burn through as they will eventually all get passed to a solo masq player. Masqing curses back becomes a collective action problem - you don't want to be the guy giving curses (at some opportunity cost), but you may have better options (like buying a stronger 3 like Swindler) so only one masq will take care of curses for the third player who wins the exchange. You can also start playing around with helping one opponent to win (match) some key split (e.g. duchies in a Duke game)
Swindler also plays weird in 3er where you have a lot easier time using it to burn provinces/colonies (thanks to Kc or something to play a bunch on the final turn). Likewise, the curses go much quicker (each swindler has 2x the chance of junking a curse) so you get fewer plays of swindler before you start swindling curses to coppers. Odds of your key cards getting Swindled (e.g. 5's to duchies, duchies to 5's, 4's to potions, 3's to silvers/swindlers, golds to garbage 6's, and 2's to estates) are a lot higher. You can also count on unique price points (4's, 7's, potion costs) running out of replacements a lot more often if Swindler is flying around so it can now read "trash something vital if you hit it".