
Petty Alchemy RPG Superstar Season 9 Top 16 |

Best would probably be Sorcerer (or another Cha caster) to maximize your options. You can use Vanishing Trick to get in a sneak attack, or you can cast a spell and disappear on the same turn.
To specialize, you could go with Monk. People like TWF with sneak attack, and the Monk gives you that with Flurry. You don't need to max Dex either, and you can once again dump Cha by using Wis for Ki.
Another good option could be Beast Totem Barbarian so long as you take Scout archetype for Ninja, then you can Sneak Attack Pounce. Not too good at problem-solving outside of combat though (for a gestalt character).

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hmm
ninja/paladin has a good mechanical synergy, but poor thematic senergy,
for something I'd actually play
for a combat heavy build with lots of tricks up my sleave I'd go the "naruto" build (I like to name my builds sometimes) I'd go ninja (glory rouge, maybe also pet trainer and/or mageslayer) 20 (or ninja 10/assassin 10)/sorcerer (shadow, maybe?) 9/monk 1 (four winds, perhaps, with the ascetic mage feat to allow you to use cha for your monk stuff) enlightened fist 10,
for a stealth focus build I'd go ninja (glory rouge) 20/ranger (trapper, falconer) 17-20, shadowdancer 0-3

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Evil???? Ninja 10/ Assassin 10/ Sorcerer 8 (Arcane Bloodline)/ Anti-Paladin 2/ Eldritch Knight 10 9th level spells.... Not many things could touch your saving throws if you use a wand of Bestow Grace. Lastly Two weapon Fighting+Smite Good+ Sneak Attack+Poisons+ Spell Critical= PROFIT!! Vanishing Trick is only there if it isn't an instant kill.
Good???? Ninja 20/Sorcerer 12/Dragon Disciple 8 Have you ever seen a vanish Trick Dragon getting sneak attacks? I think it would be funny and pretty powerful. Still have 9th level spells. You could also Paragon Surge your Shenanigans.
Another Good Combo would Be Ninja/Bard would be simple and very effective.

kBro |
Ninja/Paladin is Batman. 'nuff said.
Ninja/Antipaladin would be terrifying for the reasons mentioned above and more.
Ninja/Samurai could be very flavorful. Taking the Sword Saint archetype could be brutal single hits with all those d6's, or if you went third party the Nitoujutsu Sensei archetype for TWF sword master.
Ninja/Summoner would be ridiculous, with Synthesist being Ironman Ninja.
Ninja/Sorcerer for spontaneous arcane full casting, or Ninja/Oracle for divine.
Ninja/Bard would be interesting, but invisibility prevents visual components for performances. However there's a lot of utility there.
Ninja/Fighter for straight combat with all those bonus feats.
Ninja/Barbarian could be brutal, probably working best with Urban Barbarian.
Ninja/Ranger with any archetype that doesn't rely on WIS heavily would be an excellent scout/tracker/assassin.
Ninja/Gunslinger with the Mysterious Stranger archetype would be fun, but you'd need some oil of silence for your guns.
Ninja/Monk was already mentioned, and can be done well since you get Ki from both WIS and CHA.
Ninja/Inquisitor could be pretty effective with bane/judgement, but your CHA will suffer a bit since you'll need higher WIS.
Ninja/Alchemist could also be pretty fun with bombs, or if you went Vivisectionist you'd get double sneak attack dice, but like Inquisitor your CHA might suffer for INT.
Ninja/Magus could be fun with sneak attack + spell strike, but it has the same problem as the Alchemist with INT dependence.
Ninja/Cleric would be very effective with all good saves and full casting, but might be a little MAD.
Ninja/Druid would be very effective like the Cleric, all good saves, full casting, but very WIS dependent and CHA might suffer for Ki.
Ninja/Wizard and Ninja/Witch could be fun, but need high INT which could hurt other stats.
But this is just looking at basic class synergy. Anything with casting will be better than anything without. Anything with CHA dependence works better than INT or WIS dependence. Anything with good Fort and/or Will saves is good help. Full BAB martial with bonus feats is always better for combat.

ChainsawSam |
Ninja/Magus
Don't worry about Charisma. Keep it at 10. Maybe even drop it to 8.
When you hit level 6, pick up Ki Arcana. This will allow you to use your Ki points and Arcane pool interchangeably. You'll have plenty of Arcane Pool from int so any Ki you gain through your stunted Charisma is just icing on the cake. Use Ki for Arcane Pool, use Arcane Pool for Ki. Whatever.
Then go crazy with your gigantic stack of skills, great saves, sneak attack, and spells. It's a great combo. Not even that MAD if you go with Dervish Dance.

Azelyan |

Funny you mention this, I am playing a Kitsune Gestalt Ninja/Tattoo'd Fey Sorcerer.
She uses enchantment magic to get what she needs (favored class bonus goes into Sorcerer), and if she doesnt like the outcome she vanishing tricks and starts to use her ray magic.
Super fun build to play, since I used ninja tricks to pick up a combat trick (from rogue) for Point Blank shot, as well as precise shot for a feat. Spending more feats on spell focus/penetration for my enchantment magic. The good thing about Ray spells. is you can get your sneak attacks off with them, and most dont require a save (Or I dont pick ones that do).
So between Ray sneak attacks, and Enchantment magic, my kitsune has become a real terror of a gestalt.