Thief's win rate on Isotropic is an amazing 0.71. Case closed. I buy that card in, like, at most one percent of my games (most of the time it ends up in my deck, you can thank Swindler), and after several thousand games I have yet to encounter one where I wish I had a Thief. I've heard tales of it being useful in 4p games where you go for Gardens (but don't have the traditional enablers)... but, man, that's like a corner of a corner of a corner case. The attack is highly likely to help your opponent early on, and later in the game even if it nabs a good Treasure good luck getting to play that Treasure much. Worst of all, the same basic treasure-stealing idea was rehashed in Pirate Ship and Noble Brigand, both of which are a) obviously better than Thief, and b) also among the ten worst cards in the game. (Okay, okay, the Pirates are a little better than that in multiplayer. I still always lose on the rare occasions I try to make them work.)
A lot of votes for Transmute here, and I do think it's pretty horrible most of the time. It's certainly the one Potion card that is just about never ever worth going for as your only potion card. But I've had success using it once in awhile when there's other Potion cards about, and the wacky-Remodel can often be better than nothing as a consolation prize in decks that are swimming in either +Actions or Curses. There are, like, a couple dozen cards I buy less often than Transmute, and quite a few of them have worse win rates, and/or just as weak effects.
I do think Scout, Adventurer, and possibly Counting House deserve a special honorable mention: these two or three cards are the only ones in the game that, far as I could tell, could straight up cost less than they do without causing any balance problems whatsoever. An Adventurer at $5 or a Scout at $3 would be perfectly balanced, and Counting House at $4 might be too. (Would also make it more viable as a counter to Amb/Mountebank, since you can buy it with junkier hands, which is near as I can tell its main use.) These cards are not necessarily the next worst, but cards like Saboteur (who belongs in this discussion), Noble Brigand, and Thief would screw up games they were in if they cost any less.
Going by my buy% stats, you'd expect me to say Explorer is one of the worst. But Explorer is a card I know I overlook, and it can be useful on bad BM boards. So I grudgingly admit it's better than Sab and Counting House among $5s, and doesn't belong in the discussion here. And neither do any of the $2 or $3 cards. Even Duchess and Develop have their uses, and Chancellor is much better than its reputation. (Duchess is a great opening with Lab, for instance, and is good as a free pickup in green-card-rush games; Develop is tricky and narrow but even bad trashing is sometimes better than no trashing, and it can be a great backdoor into Grand Market and stuff like that; Chancellor rocks the house whenever Familiar or Stash are around, and sometimes well there just aren't better terminals.)
If you had to press me for a good #2 choice after Thief, I'd probably go with Adventurer or Counting House. Scout provides infintesimal value most of the time, but since it's a non-terminal it gets bought too often (say, near the end of Vineyards games); Adventurer and Counting House are expensive terminals that require incredibly specific (and normally awful) situations in which to shine. Saboteur is probably worse than them more often, and its win rate is also worse given that it is mostly a desperation buy, but the 2 percent of games where it can go nuts with King's Court and/or Minion disqualify it. Noble Brigand has my worst win rate and I buy it second-least, but it's close enough to a "strictly better Thief" that it's disqualified. I guess Adventurer has to be my #2, because jeez it costs $6. Counting House and Scout at least have other cards which cost the same and are just as bad, but Adventurer is simply without peer.