Dominion - Defeating the Alchemist
In the short term, cards that make him discard cards are the best way to go.  Minion is the best because it makes him discard all of them:


Other cards that help in the short term:



(sadly, Ghost Ship does not)

In the long run, there are several strategies:


If Embargo is in play, Embargo Alchemist early on.

Destroy his cards using Saboteur or Swindler.
 
Destroy or steal his money using Thief or Pirate Ship.  Note: These two cards will also flip his top two cards even if they aren't money.
 
Give him Curses, or use Ambassador to give him unhelpful cards.



One last note: Each time he buys an Alchemist, he's buying another action card.  If he's buying action cards, he's not buying money cards.  As bad as it sounds, Alchemist-heavy can often be defeated by Big Money decks, even if they have 5 Alchemists in their hand (and thus essentially start with 10 cards).

Also, make sure he isn't putting the Alchemists on top during turns he doesn't have a Potion in play.

Edit:
It's been a while, but one thing I noticed I forgot to mention when I answered this in 2010: Alchemist is only +1 Action, which means unless they have a +2 Action card somewhere, they only have one action at the end of the chain.