Well, there are plenty of deck available in ML to counter zoo decks, but I must admit AI can play them very well as long as he have the lands to do it

For example, you can take a classic Scepter Control deck like the one made by awww1979:
- Code: Select all
;0-Scepter Control
;Blue/White
;User
;User E-Mail
;14/07/2009
;1
;4th Edition
;
.1 1 Ancestral Recall
.585 3 Boomerang
.4996 1 Fact or Fiction
.720 4 Mana Drain
.1455 4 Memory Lapse
.1084 1 Merchant Scroll
.1527 1 Mystical Tutor
.10 1 Balance
.64 2 Disenchant
.672 1 Holy Day
.240 4 Swords to Plowshares
.290 3 Wrath of God
.1291 2 Iridescent Angel
.9627 4 Plumeveil
.6632 3 Chrome Mox
.6690 4 Isochron Scepter
.167 1 Mox Pearl
.169 1 Mox Sapphire
.230 1 Sol Ring
.1487 4 Flooded Strand
.1713 4 Hallowed Fountain
.694 1 Karakas
.2305 1 Kjeldoran Outpost
.438 1 Library of Alexandria
.254 4 Tundra
.126 4 Island
Lot of removal, sword weenie, unlimited counter with Isochron and Outpost and Angel as finisher
A more recent and standard one is Jace Nin deck, though a bit harder to play since it's way slower than the above :
- Code: Select all
;Jace, Stealer of Staffs
;NetDeck
;Demarge
;PlayDeckAnalyser@slightlymagic.net
;dec. 13, 2012
;1
;4th Edition
;This PlayDeck was imported from NetDeck by PlayDeck Analyser v0.4b
.12661 3 Azorius Charm
.12695 1 Cyclonic Rift
.2452 3 Dissipate
.770 1 Remove Soul
.11945 3 Feeling of Dread
.9395 1 Negate
.12788 1 Psychic Spiral
.12451 1 Righteous Blow
.12834 2 Sphinx's Revelation
.12843 3 Supreme Verdict
.12483 3 Terminus
.12623 3 Staff of Nin
.12662 3 Azorius Guildgate
.8212 4 Ghost Quarter
.10419 4 Glacial Fortress
.1713 4 Hallowed Fountain
.126 6 Island
.188 5 Plains
.12757 2 Jace, Architect of Thought
.11821 2 Jace, Memory Adept
.12479 1 Tamiyo, the Moon Sage
.12704 2 Detention Sphere
.12771 1 Martial Law
.12079 1 Snapcaster Mage
Still, my current favorite control deck is Black Control : Consuming Vapor inspired from Innistrad :
- Code: Select all
;Consuming Vapors2
;Black
;Player
;no@spam.com
;02/11/2011
;1
;4th Edition
;
.11417 3 Black Sun's Zenith
.10892 4 Consuming Vapors
.1588 4 Corrupt
.1275 3 Damnation
.55 4 Dark Ritual
.68 3 Drain Life
.10542 4 Gatekeeper of Malakir
.1592 4 Tendrils of Corruption
.812 1 The Abyss
.1226 1 Visara the Dreadful
.12147 2 Chalice of Life
.166 1 Mox Jet
.1467 3 Wayfarer's Bauble
.1505 2 Cabal Coffers
.239 21 Swamp
Gatekeeper for removal and chump blocker, Consuming Vapor as slower since AI will not cast anything fearing rebund if vapor is out, lot of mana acceleration like ritual, bauble, coffer, the abyss to shut down weenie and Visara/Chalice as finisher.
I also did a Sanguine Bond version, it's a very fun deck once it's out

In the same theme, AI do wonderful job with BGR Jund as long as it can get out a Forest or Savage Lands, else it will die pitifully with nothing in play.
- Code: Select all
;BGR Jund
;Red/Green
;User
;User E-Mail
;03/08/2011
;1
;4th Edition
;
.145 4 Lightning Bolt
.282 1 Wheel of Fortune
.9148 4 Garruk Wildspeaker
.10244 4 Bituminous Blast
.10246 4 Bloodbraid Elf
.1442 4 Broodmate Dragon
.10309 4 Maelstrom Pulse
.10330 4 Putrid Leech
.10078 4 Sprouting Thrinax
.1471 4 Terminate
.17 1 Black Lotus
.165 1 Mox Emerald
.166 1 Mox Jet
.168 1 Mox Ruby
.9 4 Badlands
.1488 4 Bloodstained Mire
.1204 4 Savage Lands
.1473 4 Wooded Foothills
.91 1 Forest
.164 1 Mountain
.239 1 Swamp
The advantage of BGR Jund compared with RG Zoo is that AI can destroy anything hindering him with Maelstrom Pulse, while RG Zoo cannot if shut down by an enchantment or an artifact. It's also one of the fastest deck I know in the ML deck pool that can match nearly any type of deck if well played (of course it cannot match broken deck like Dredge or Natural Order...).