Chalice is simply disruption. IMHO one of the best disruption spells ever. The card should be cast with enough counters on it to stop a significant number of cards in your opponents deck. What to set it on?
vs. Sligh: 1 counter nullifies most of the deck
vs. most anything blue: 1 counter stops key spells like Ancestral, Brainstorm, Mystical Tutor, etc.
vs. most anything blue: 2 counters nullifies quite a bit of their permission (counterspell, manadrain, possibly others), and possibly draw and tutor spells (depending on their exact build), also nullifies that pesky Fire/Ice.
vs. combo: if set correctly, Chalice outright kills most combo decks. Set at 0 or 1 and Long (including the new post-Jan builds) pretty much dies immediately. Set at 2 and Dragon is pretty much dead (3 may also be a good choice, depending on how many Necromancies your opponent runs).
vs. Hulk/Tog: in addition to the comments on killing blue (above), a Chalice at three stops Deed, Tog, and Cunning Wish...so it neuters most Tog builds quite nicely.
In addition to nullifying a good portion of your opponents deck, look at what most Workshop decks lose to a Chalice set at these levels:
1 counter -- Welder, a key card. Depending on the match-up it may be best to drop the Welder before a Chalice at 1 (against something akin to Long, probably not though).
2 counters -- Sphere. To shut down opponents permission as well as some tutor, draw, and board control...this is a no brainer (you lose 4 cards out of your deck, they lose most of their deck). Some Workshop builds will also lose Winter Orb at this level...make the choice on whether this will screw up your opponent more than you.
3 counters -- Tangle Wire. Again you are losing a stall card, they are probably losing most of the key cards in their deck.
Workshop decks play above the traditional mana-curve, so setting Chalice's will 0 through 3 counters will normally wreck opposing (non-Workshop) decks and only modestly interfere with your own.
Obviously you have to be able to decipher your opponent's deck early on to make use of this card. If you are new to the game, or face a very random metagame, it may be best to stay away from Chalice. But if you have a reasonable chance of being able to understand what your opponent is trying to do from the first few turns of a match, Chalice can be a game breaking play. (Scouting helps!

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