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Blue and Black Ninja deck. This deck did very well in FNM tourneys back when Rav/Kamigawa was the current cycle. I added the snowlands when Coldsnap came in. Just use the unblockable creatures to bring in the Ninjas, and use the Jitte. Mid Game Moroii and Late Game Ink-Eyes Rat with Cleavage for the win :) Counters and creature removal will add control. If you need more counters just add from sideboard. Also replace Nezumi Cutthroat with the Bog Imp in case you're playing against Black.
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although that is the best way to use ninjustu, the cards you use to "support" your ninjas arent the best....
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I ran a ninja deck too back when it was standard legal. Run a full playset of Ornithopters for sure....they are by far a ninja's best friend since you can redrop them after they've been substituted with ninjitsu in Main Phase 2. Also Higure (the legendary blue ninja) helps you find your other ninjas and adapt to the situation. I also found a playset of Will-o-the-Wisp to be very useful if you don't have an Ornithopter in hand since it costs only 1 black to play, and it can block for you and regen. Lastly, Ronin Warclub is a-freakin-mazing in ninja decks since once a ninja comes in via ninjitsu, the club immediately attaches to them and comes in for more damage. Then redrop the Ornithopter or Will-o-the-Wisp and then your opponent has a 2/3 flying or 2/2 flying regen blocker to deal with. Rinse and repeat :D.
I always considered a ninja deck to be a deck that burned with creatures instead of red spells. If you don't win by mid-game your in bad shape, but it usually goes off fast like a burn deck. At least that's how I built mine.
At the time that is why I had the Moroii as support, a 4/4 flyer for its cost can pack a punch. I'm very fond of the deck :) Hark, what cards do you recommend?