-- Master of all Trades --
Wanted to explore Greninja's infinite range of options.
Italicized options are primarily useful on
Mega Greninja with its Technician
Nasty Plot is probably the quintessential Greninja move (unless you run Specs or Scarf which are both viable). This turns you into a death machine. If you're Mega, you're now smashing everything with Dragapult speed, if you're Bond, they can't deny your +1 Spa/+1 Spe for long. Only very, very strong special walls like Mega Floette can safely stop a +2 Greninja -- that or just clicking Extreme Speed with 2 separate mons
Hydro Pump/Surf/Water Pulse/Scald: basic primary STAB option. At +2, your water moves will oneshot most neutral targets.
With Pump vs. Surf/Water Pulse (which has 20% confuse chance), it's the usual deal: some bulkier mons are a kill/roll with Pump but a roll/not even a kill with Surf. For example a bulky Zygarde:
+2 252 SpA Greninja-Mega Hydro Pump vs. 252 HP / 0 SpD Zygarde: 382-450 (90.9 - 107.1%) -- 43.8% chance to OHKO
+2 252 SpA Greninja-Mega Surf vs. 252 HP / 0 SpD Zygarde: 313-369 (74.5 - 87.8%) -- guaranteed 2HKO after Leftovers recovery
Water Shuriken: can be used as in addition to the water STAB, or instead of it. The main issue with using it as the main water STAB is it's not reliable as a primary STAB, especially outside of mega (where it's a 30-75 power move, average 46.5, compared to 90 for Surf).
But as a priority move, well a 46.5 BP priority move that can be boosted by Technician is fearsome, and if you roll well and get 4 or 5 hits you can even hit 90 or 112.5 BP, which is sufficient to kill most sweepers if they've been chipped.
252 SpA Technician Greninja-Mega Water Shuriken (15 BP) (5 hits) vs. 0 HP / 4 SpD Gallade-Mega: 165-200 (59.5 - 72.2%)
Notably Water Shuriken also griefs Mega Barb, after a Shell Smash and/or Close Combats it usually is forced out or killed by Shuriken
Dark Pulse/HP Dark: Dark STAB. Both are good options in Mega, the flinch chance of Dark Pulse gives you a shot at bullshitting your way through a check, and although it precludes other Hidden Powers, HP Dark is more powerful, for example giving you a roll against targets that would otherwise live:
252 SpA Technician Greninja-Mega Hidden Power Dark vs. 252 HP / 4 SpD Slowbro: 360-426 (91.3 - 108.1%) -- 50% chance to OHKO
252 SpA Greninja-Mega Dark Pulse vs. 252 HP / 4 SpD Slowbro: 320-378 (81.2 - 95.9%) -- guaranteed 2HKO
Dark power is useful against Aegislash, Espeon, MFroslass, Gengar, Gourgeist, Meowstic, Megagross (HP Dark is a roll to OHKO), Mega Star, Slowbro, and Glowking, among others, and it hits many Water resists neutrally too
Ice Beam/Icy Wind: Ice Beam is used to OHKO Zygarde and the rare Grachomp, devastate Dragonite (and if someone is running the mega they get OHKOd too), and as coverage to hit various odds and ends: notably Chesnaught and Mega Meganium (who resist both water and dark), plus some of the mons who resist water (Grasses, other than the rare Abomasnow, and Dragons not named Hoodra or ZardX).
Icy Wind is for megas only, and although I've never seen it it looks good in practice. It's a bit weaker and has 5% miss chance, but in exchange you can slow down a sweeper you can't OHKO so that it can be taken down by something else.
On the lower power: sometimes it could be an issue
252 SpA Greninja-Mega Ice Beam vs. 252 HP / 0 SpD Zygarde: 420-496 (100 - 118%) -- guaranteed OHKO
252 SpA Technician Greninja-Mega Icy Wind vs. 252 HP / 0 SpD Zygarde: 384-452 (91.4 - 107.6%) -- 50% chance to OHKO

alternatively:
Sludge Wave can be used to take on those who would dare try to check Greninja. Clefable, Floette, Mega Audino, and Chesnaught are hit for big damage, and Meganiums are wiped from existence.
252 SpA Greninja-Mega Sludge Wave vs. 252 HP / 4 SpD Clefable: 230-272 (58.3 - 69%) -- guaranteed 2HKO -- Greninja demands SpDef clef, but everyone else demands physdef, it's lose/lose
252 SpA Greninja-Mega Sludge Wave vs. 252 HP / 252+ SpD Floette-Eternal: 128-152 (36.3 - 43.1%) -- guaranteed 3HKO
Also if you run non-mega sets or are in Protean pre-mega, you can do some heinous things. I used to run Specs Protean and had the pleasure of oneshotting a Clef:
252 SpA Choice Specs Protean Greninja Sludge Wave vs. 252 HP / 4 SpD Clefable: 432-510 (109.6 - 129.4%) -- guaranteed OHKO
(Sludge Bomb is not used because it completely blanks into Chesnaught. Also, the purpose of the Poison coverage move is the raw power to put down fairies, although if you are lucky enough to get a poison it would be worth)
Flip Turn/U-Turn are good moves. U-Turn is for Protean, you can do some serious damage to Slowbros and Meowstics while pivoting, while Flip Turn when boosted by Technician on 125 base Atk from MGren lets you leave any bad matchup at will.
4 Atk Technician Greninja-Mega Flip Turn vs. 252 HP / 0 Def Floette-Mega: 133-157 (37.7 - 44.6%) -- guaranteed 3HKO
Hidden Power Electric/HP Grass/Grass Knot: 3 moves useful mostly for the Mega (Technician HP is 90 BP), which help you with waters. This means Vaporeon, rival Greninjas (both 60 BP = 90 BP grass knot), Blastoise and Sharpedo (80 BP), Megasharp (100 BP), and MGyara (who walls you, and even 120 BP Grass Knot is only a 2HKO).
(And although you should switch out of Mega Gatr, if you have to fight then Grass Knot is the best reliable option you have:
252 SpA Greninja-Mega Grass Knot (100 BP) vs. 0 HP / 0 SpD Feraligatr-Mega: 119-140 (38.2 - 45%) -- guaranteed 3HKO)
HP Elecrtic is IMO better, you can surprise OHKO a Gyarados switching in (or a fake mega gyarados), and if a Volcanion fights you it will regret it.
252 SpA Technician Greninja-Mega Hidden Power Electric vs. 252 HP / 0 SpD Volcanion: 218-258 (59.8 - 70.8%) -- guaranteed 2HKO
You also 2HKO Skarm, MegaLucha, and Mega Pinsir (but you 2HKO them all anyways, just with a little less damage)
HP Grass's advantage over Electric is in the Barbaracle mindgame: when Mega Barb decides to not mega to live Surf/Hydro Pump, you can oneshot it with HP Grass
252 SpA Technician Greninja-Mega Hidden Power Grass vs. 252 HP / 0 SpD Barbaracle: 452-536 (129.8 - 154%) -- guaranteed OHKO
And if it does mega, you still cope into some damage (Surf doesn't kill Megabarb either, only Pump does)
252 SpA Greninja-Mega Grass Knot (100 BP) vs. 252 HP / 0 SpD Barbaracle-Mega: 212-250 (60.9 - 71.8%) -- guaranteed 2HKO
One rarely mentioned advantage of Hidden Power is that you can only infer what type it is, which is an advantage over moves like Grass Knot. They don't know if it's HP Dark or HP Electric until they look in the box (me when secret HP Fighting)
Psyshock is an option, I haven't used it before, but it might be able to force past special walls (especially Mega Dragalge who is Psychic-weak)
252 SpA Greninja-Mega Psyshock vs. 252 HP / 0 Def Floette-Eternal: 124-146 (35.2 - 41.4%) -- guaranteed 3HKO
252 SpA Choice Specs Protean Greninja Psyshock vs. 252 HP / 0 Def Floette-Mega: 187-222 (53.1 - 63%) -- guaranteed 2HKO
And it hits Mega Lopunny and Venusaur
Mud Shot is funny, it lets you do things like troll MegaMetagross if you can't oneshot it, by lowering its speed to revengekill territory. Also it hits Hoodra, but only for pathetic damage because it's Hoodra:
252 SpA Technician Greninja-Mega Mud Shot vs. 248 HP / 8 SpD Assault Vest Goodra-Hisui: 86-102 (23.6 - 28%) -- 83.3% chance to 4HKO

Oh but Greninja can also run mixed, where it has Swords Dance and Low Kick (kills Hoodra) and Gunk Shot and Liquid and UTurn/Technican boost Flip Turn, Power-Up Punch, Shadow Sneak and Rock Tomb and Aerial Ace and Feint Attack and Trailblaze. But the post would be too long