I quite like the Ninja I made using Tome of Battle, and it's proved balanced and fun in play. From my sig:
[sblock]Ninja of the Sublime Way
Hit Die: d6
BAB: Medium
Saves: Good Reflex, Poor Fortitude and Will
Skills: 6+ int mod (x4 at first level)
List: Balance, Bluff, Climb, Disguise, Heal, Hide, Intimidate, Jump, Knowledge (local; nobility and royalty), Listen, Martial Lore, Move Silently, Open Locks, Profession, Sense Motive, Sleight of Hand, Spot, Swim, Tumble
Proficiencies: No armor or shields, Simple weapons, sai, shortsword (Ninja-to), siangham, shortbow, kama, nunchaku, shuriken, and hand crossbow.
Disciplines: Desert Wind, Shadow Hand, Setting Sun, Tiger Claw
Recovery: Run or Withdraw action recovers all readied maneuvers
Maneuver swapping: At levels 4, 6, 8, 10, 12, etc...
Ninja Class Features by level:
[sblock]
Code:
Maneuvers
Lvl K / R / S Special Speed Burst
1 3 3 1 Quick to Act +1, Weapon Focus (SH), AC Bonus --
2 4 3 1 Acrobatics, Improved Unarmed Strike --
3 5 3 1 SS +1d6 +10 ft
4 5 4 1 Insightful Strikes (SH), Uncanny Dodge +10 ft
5 6 4 2 Quick to Act +2 +20 ft
6 6 4 2 SS +2d6 +20 ft
7 7 4 2 Poison Use +30 ft
8 7 4 2 Defensive Stance (SH) +30 ft
9 8 4 2 SS +3d6, Evasion +40 ft
10 8 4 3 Quick to Act +3 +40 ft
11 9 5 3 Ninjutsu Focus +50 ft
12 9 5 3 SS +4d6, Eternal Calm +50 ft
13 10 5 3 Lethal Cut +60 ft
14 10 5 3 Ninjutsu Focus +60 ft
15 11 6 3 Quick to Act +4, SS +5d6 +70 ft
16 11 6 4 Nondetection +70 ft
17 12 6 4 Ninjutsu Focus +80 ft
18 12 6 4 SS +6d6 +80 ft
19 13 6 4 Silencing Strike +90 ft
20 13 7 4 Quick to Act +5, Stealth Dash, Ninjutsu Focus +90 ft
[/sblock]
Quick to Act: The Ninja recieves a bonus on his initiative checks.
Shadow Hand Focus: As a Swordsage's Discipline Focus, the Ninja instead gains these features solely for the Shadow Hand discipline, with new abilities entirely at levels 12 and 16.
AC Bonus: Ninja's receive a bonus to armor class as a monk of their level (See Monk). Monk level stack with Ninja levels for determining the level bonus to AC.
Acrobatics (Ex): Add wisdom bonus to Balance, Climb, Jump, and Tumble checks. This only functions while unarmored and unencumbered.
Improved Unarmed Strike: The Ninja gains Improved Unarmed Strike as a bonus feat.
Speed Burst (Su): Initiated as a swift action, this boosts the Ninja's speed by the listed amount until the start of his next turn. Can only be used unarmored and unencumbered.
Sudden Strike: As Sneak Attack, with the following exceptions. Flanking does not allow a Ninja of the Sublime Way to use Sudden Strike. Concealment less than total concealment does not prevent a Ninja of the Sublime Way from using Sudden Strike.
Uncanny Dodge: As the Rogue class feature.
Poison Use: A Ninja of this level no longer risks poisoning himself when applying it to his weapon.
Eternal Calm: The Ninja is always focused, never distracted. He may always choose to take ten on Hide and Move Silently checks.
Ninjutsu Focus: Choose one of the following.
∙Crippling Strike (Ex): As the Rogue Special Ability
∙Defensive Roll (Ex): As the Rogue Special Ability
∙Opportunist (Ex): As the Rogue Special Ability
∙Hide in Plain Sight (Su): As the Shadowdancer class feature
∙Death Attack (Ex): You gain a Death Attack, as the Assassin class feature, except that it can be used at any range you could make a Sudden Strike, and the save DC is equal to 10 +1/2 Ninja level +Wisdom modifier. In addition, whenever you attack with a poisoned weapon, the poison’s save DC increases by 2.
∙Harbinger of Death (Ex): Whenever you drop a foe with Sudden Strike (reducing her to negative hit points or destroying her), all other foes within 30 ft must make a Will save, DC 10 + ½ Ninja level +Wisdom modifier. Creatures with HD equal to or less than the felled target become frightened on a failed save, shaken on a successful save, for one round per Ninja level in either case. Creatures with greater HD than the one you have slain must save or become shaken for one round per Ninja level, with no ill effect on a success.
Find Pressure Point (Ex): You gain a 25% chance of dealing Sudden Strike damage to creatures immune to it (by any means), and reduce any chance the target has of ignoring your SS damage by -25%. Note: You can take the feat Improved Pressure Point up to 3 times. Each time it is taken, these percentages increase/decrease by 25%.
∙Running Climb (Ex): Move up a wall as a move action at your full speed. If you do not reach a horizontal surface to stand on after this movement, you immediately fall, unless you catch yourself with the Climb skill. Falling in this way, you may not “jump off” to reduce falling damage, though you may tumble upon landing. One creative use for this could be to set up a falling attack for more damage, at great personal risk.
∙Sniper’s Eye (Ex): You are so well trained in ranged assassination, “point blank” range is now considered 100 ft for you, modifying the range limit on that feat and any precision-based attack you know. If you succeed in your Hide check after a sniping attempt, you may shift your position up to 5 ft per 5 points your Hide check exceeds 10, up to a maximum of your speed.
∙Springing Attack (Ex): You gain the benefits of the Spring Attack feat. If you already possess (or later obtain) that feat, you instead gain the ability to take any standard action between your movement. Thus, you could move up, use a standard action strike maneuver, then retreat away, for example.
Lethal Cut (Ex): Add your wisdom bonus to attack and damage whenever you make a Sudden Strike attack. The wisdom bonus to damage stacks with that from Insightful Strikes if doing a SH strike maneuver.
Nondetection (Su): You are constantly under a Nondetection effect, as the spell. This can be suppressed or resumed at will as a free action. Caster level is equal to your Ninja level, and since you are considered to have “cast” it on yourself, caster level check DC to pierce it is DC 15 + your Ninja level.
Silencing Strike (Su): Anyone hit by your Sudden Strike must make a Fortitude save (DC 10 + 1/2 Ninja level + Wisdom mod) or become Silenced for the next 1d4 rounds.
Stealth Dash (Su): Whenever you initiate your speed burst, you gain partial concealment (20%) for one round, and if you gain partial concealment from another source (Child of Shadow stance, fog, etc...), it stacks with this to give full concealment (50%) while both are active. If you move after initiating the speed burst, you may make a free hide check at the end of the movement, as part of the move action, provided you are in an area you could normally hide in. Finally, 3/day, you may use stealth dash to also grant you an effect similar to Mislead (caster level = ninja level). The greater invisiibility and the major image both last for one round, instead of the normal durations. This is initiated as a free action as part of stealth dash. It is considered a 9th level spell-like ability.[/sblock]
And the equivalent to the Rogue's Savvy Rogue feat (C.Scoundrel), the Master Shinobi feat:
[sblock]Master Shinobi
You have mastered one or more of your Ninjutsu Focus abilities.
Prerequisite: Ninja of the Sublime Way level 11th
Benefit: Based on the Ninjutsu Focus abilities you have, you gain one or more special benefits described below. You gain the benefits for all Ninjutsu Focuses you have, even ones gained after taking this feat.
Crippling Strike: As the benefit from Savvy Rogue.
Death Attack: You gain a +2 competence bonus on the Death Attack save DC.
Defensive Roll: As the benefit from Savvy Rogue.
Find Pressure Point: Your chance of dealing SA/SS damage also applies to your chanes of delivering a critical hit, even if the creature is normally immune.
Harbinger of Death: You gain +1d6 to your Sudden Strike damage against any target that is suffering from fear (Shaken or worse), regardless of the source of fear.
Hide in Plain Sight: A number of times per day equal to your Wisdom modifier, after successfully hiding within a shadow, you can transfer to another shadow which you have line of effect to as a free action. The new location must be within 10 ft per Ninja level.
Opportunist: As the benefit from Savvy Rogue.
Running Climb: You can use Feather Fall as a spell-like ability a number of times per day equal to your Wisdom modifier, CL equal to your Ninja level.
Sniper's Eye: Once per day, you can reroll the attack roll of a ranged sneak attack that missed its target. You must take the result of the new roll, even if it is worse than the first one.
Springing Attack: You gain a +2 competence bonus on the attack roll when attacking with this ability.
Untraceable: When any power or effect takes hold over your mind, you can delay the effects for a short while. This protects against anything the Mind Blank spell would, except it merely delays the onset of such a condition, instead of blocking it outright. Use of this ability requires no concious effort and is automatic, at which point you become aware it is active, though not necessarily what caused it to become active. This ability can be used Wisdom modifer times per day, for a total number of rounds per day equal to your Ninja level, whichever runs out first.[/sblock]