Discussing various base class concepts sort of cross polinated with my desire to experiment with my new attribute/skill array and gave me a little burst of creative energy. So, here you go

!
The paths are sort of placeholders against new ones more closely tailored to traditional ninja-y goodness (I'd like to do a shuriken throwing path for them

). I'll post up a standard array version after any discussion here dies down for inclusion in the compendium.
The New Pie can be found here:
http://www.crafty-games.com/forum/index.php?topic=6692.0NINJA The quintessential stealth operative, the ninja is equal parts spy and assassin.
In your campaign, a Ninja could be…
• A loyal retainer eliminating threats to his honorable master
• A shadowy mercenary feared as much as he is respected
• A cruel enforcer of a dark regime based on terror
• The guardian of a secluded tribe and their deadly traditions
• A secret warrior locked in a battle between rival clans.
Party Role: Specialist/Combatant. A ninja's first concern is secrecy, but when discovered they can prove more than a handful for such diligent guards...
Class Features Favored Attributes: Fitness & Awareness
Class Skills: Acrobatics, Acting, Athletics, Competition, Focus, Investigate, Mischief, Profession, Sense Motive, Stealth, Tactics, & Vigilance
Skill Points: 8 + Guile modifier
Morale: 6 + Determination modifier per level
Starting Weapon Proficiencies: 5 + Precision modifier
Core Ability Superior Fitness: When you spend an action die to boost a Fitness skill or melee/unarmed attack check, roll 3 dice and keep the single result you prefer.
Class Abilities Get In, Get Out: At Level 1, your Athletics and Stealth are flawless.
(Flawless. Each time you fail a check with a flawless skill and don’t suffer an error, you still succeed as long as the check DC (or your opponent’s check result) is equal to or less than your Class Level + 20. If several grades of success are possible, you achieve only the lowest possible positive result.
If you gain the same flawless skill from two or more classes, add together your Class Level in all of those classes when determining the minimum result.) Silent Killer I: At Level 2, you do not need to make an attack check when making melee attacks against standard characters out of combat - you automatically hit (this cannot result in a critical hit, however). Opponents who have become aware of you cease to be aware of your presence if you remain
hidden for 1 minute even if they remain in combat. You also gain the following trick.
Silent Kill (Melee Attack Trick): If the target is a standard opponent unaware of your presence, he immediately fails his Damage save (damage isn’t rolled). Opponents defeated by this attack make no sound and do not cause other opponents to become aware of your presence. You gain 1 Edge when you defeat an adversary with Silent Kill.
Silent Killer II: At Level 11, your reach increases by 1 when making melee attacks against standard characters. You now gain 2 Edge when you defeat an adversary with Silent Kill.
Silent Killer III: At Level 19, your reach increases by an additional 1 when making melee attacks against standard characters (for a total of +2 reach). You now gain 3 Edge when you defeat an adversary with Silent Kill.
The Way of Shadows: At Levels 3, 5, 7, 9, 11, 13, 15, 17, and 19, you take a step along the path of Darkness, Shuriken, Spirits, or Travel. If you have an alignment, you may add exactly one path from that alignment to this list (chosen the first time you take a step along one of those paths with this ability). If you gain the ability to cast a spell from The Way of Shadows, your caster level is considered equal to you Ninja Class Level
only, ignoring any other caster levels you may have.
Ninjutsu I: At Level 4, you gain a dodge bonus to defense against ranged attacks equal to your Edge.
Ninjutsu II: At Level 8, you may automatically escape bonds of with a strength of 3 dice or less.
Ninjutsu III: At Level 12, you become an expert with 1 Ninja Class Skill.
(Expert. Taking 10 with this skill doesn’t take twice as long and taking 20 takes only 10 times as long.) Ninjutsu IV: At Level 16, you may spend Edge points as if they were action dice to boost checks and confirm criticals with the Athletics and Stealth skills.
Ninjutsu V: At Level 20, You gain DR equal to your Edge.
Shadow Warrior: At Level 6, once per adventure, you may spend 1 hour practicing to gain 1 temporary Covert feat of your choice until the end of the current adventure.
At Levels 9, 12, 15, and 18, you may use this ability 1 additional time per adventure.
Avoidance Technique I: At Level 10, your Awareness rises by 1. Also, when you or a hero who can see and hear you makes a Reflex save and the result is less than your Awareness, the result becomes equal to your Awareness. Leaving behind a log wrapped in your clothes is optional.
Avoidance Technique II: At Level 20, your Awareness rises by 1 (total increase 2), and this ability applies to both Reflex and Will saves.
Knife in the Dark: At Level 14, your hurled, melee, and unarmed damage rolls gain sneak attack dice equal to one-half your Ninja class level (rounded down).
Table 1.0: The NinjaLevel BAB Fort Ref Will Def Init Lifestyle Legend Abilities
1 +0 +0 +2 +1 +2 +1 +0 +1 Get In, Get Out;
Superior Fitness2 +1 +0 +3 +2 +3 +1 +0 +1 Silent Kill I
3 +2 +1 +3 +2 +3 +2 +1 +2 The Way of Shadows
4 +3 +1 +4 +2 +4 +2 +1 +2 Ninjutsu I
5 +3 +1 +4 +3 +5 +3 +1 +3 The Way of Shadows
6 +4 +2 +5 +3 +6 +4 +2 +3 Shadow Warrior 1/adventure
7 +5 +2 +5 +4 +6 +4 +2 +4 The Way of Shadows
8 +6 +2 +6 +4 +7 +5 +2 +4 Ninjutsu II
9 +6 +3 +6 +4 +8 +5 +3 +5 Shadow Warrior 2/adventure; The Way of Shadows
10 +7 +3 +7 +5 +9 +6 +3 +5 Avoidance Technique I (reflex)
11 +8 +3 +7 +5 +9 +7 +3 +6 Silent Kill II; The Way of Shadows
12 +9 +4 +8 +6 +10 +7 +4 +6 Ninjutsu III; Shadow Warrior 3/adventure
13 +9 +4 +8 +6 +11 +8 +4 +7 The Way of Shadows
14 +10 +4 +9 +6 +12 +8 +4 +7 Knife in the Dark
15 +11 +5 +9 +7 +12 +9 +5 +8 Shadow Warrior 4/adventure; The Way of Shadows
16 +12 +5 +10 +7 +13 +10 +5 +8 Ninjutsu IV
17 +12 +5 +10 +8 +14 +10 +5 +9 The Way of Shadows
18 +13 +6 +11 +8 +15 +11 +6 +9 Shadow Warrior 5/adventure
19 +14 +6 +11 +8 +15 +11 +6 +10 Silent Kill III; The Way of Shadows
20 +15 +6 +12 +9 +16 +12 +6 +10 Avoidance Technique II (reflex & will); Ninjutsu V
Path of ShurikenYou are a master of the small but deadly weapons often known as 'throwing stars'
Shuriken I: You may attack with shuriken on your person without readying them. When you defeat an adversary with a thrown shuriken you gain 2 Edge.
Shuriken II: When you throw shuriken they inflict 1d6 lethal damage and their damage cannot be reduced to less than 1 by DR and Resistances.
Shuriken III: Each round you may spend up to 3 Edge to make that many free attacks with shuriken.
Shuriken IV: Any opponent you hit with 3 or more shurikens in a single round becomes
entangled until he moves at least 10 ft. from that square or spends 2 handle item actions to free himself.
Shuriken V: You may spend 1 Edge to "reveal" that you have 10 normal shuriken on your person. No amount of searching you or removing your gear can prevent you from revealing shuriken this way.