>>17104737U-Turn (for scouting mostly, but continual U-Turn damage will add up quickly)
Surf (although Hydro Pump is its hardest hitting non-recharge special move the damage nerf and low accuracy makes Hydro Pump less attractive nowadays)
Dark Pulse (to take care of ghosts, just be careful of Sacred Sword)
Ice Beam / Hidden Power Fire / Hidden Power Ground (I've tried all of these with success)
The last move is really up to you and what your team needs. Ice Beam destroys Dragons and some flying types. Hidden Power Fire annihilates Scizor, Ferrothorn, and Genesect. Hidden Power Ground takes care of things like Magnezone and Heatran.
No matter what type of Greninja you opt to run, I suggest running a speedy nature. The meta game doesn't take kindly to slow frail attackers unless they have a really good ability to increase their longevity.
Physical Attacker - Jolly Nature (all physical moves) [gives +SPE -SPA]
Mixed Attacker - Hasty Nature (U-Turn and special Moves) [gives +SPE -DEF]
Special Attacker - Timid Nature (all special moves) [gives +SPE -ATK]
Out of the three natures listed, the last two are the ones I recommend most. As I said earlier, physical is viable, but why would you want to? Everything his physical set CAN do, other Pokemon can do much better.
