*Updated for U12*
The initial build concept for the Ninja Assassin was after U5 and involved a shortsword using Assassin II / Ninja I. At the time, I felt that shortswords were superior due to the limitation of handwraps in bypassing DR, a lack of endgame / epic handwraps, and stunning fist being limited to monk levels for calculating DC.
Obviously, all of those things have changed. Stunning fist now uses *character* levels to determine DC; DR isn't as much of an issue now with Artificer spells and adamantine-studded and silver-threaded handwraps dropping; and endgame handwraps now exist in the form of eWraps of Endless Night, eCalomel handwraps, and of course, Alchemical Handwraps.
So, without further ado, here goes:
Level split : 13 Rogue / 6 Monk / last level doesn't matter much, but suggest /1 Ranger for run speed, resistance clicky, and a free +3 damage vs. 1 FE. Additionally, 13 Rogue / 7 Monk is an option too as /7 Monk provides Wholeness of Body, and enhancements of Improved Recovery II.
Race : Half-Elf gets the nod here. Half-Elf can go Fighter Dilletante for a bonus +2 to stunning fist, while still retaining human versatility and human improved recovery enhancements.
Starting stats: Not bothering listing unless requested, since it now varies wildly with TR build points, tomes available, and how you want to play this character. Suffice to say, STR, CON, and WIS are primary stats. DEX of 17+ required for the TWF line, so however you want to get there. And lastly an INT of 12+ strongly required to keep those skills up.
Toughness, TWF, ITWF, GTWF, IC:Bludgeoning, PA, CE, Stunning Fist, Dodge, +1 (past life feat Monk or Rogue would be fantastic choices).
CE can be swapped out if you don't want to bother aiming for AC, although this build can easily obtain *fantastic* AC, and be converted into a quasi-tank. The only thing lacking will be core hps due to 13 levels of a d6 class.
Dodge is to qualify for Ninja I.
AC can easily reach 70+ self-buffed after a bit of farming. Combined with Shadow Fade (25% incorporeality) and the ability to UMD Displacement scrolls, this character is pretty hard to hit.
With Monk improved recovery II, Human (i.e. Half-elf) improved recovery II, Rogue wand and scroll mastery, and any other healing amp gear you may have, you should be able to easily self-heal via Heal scrolls for a sizeable amount.
Sneak attack damage = 10d6 (13 Rogue + Assassin II + Ninja Spy I) + 12 (sneak training IV) + 8 (backstabbing +5 item) + 5 (eRing of the Stalker).
Average sneak damage if my math is correct would be +60. +70 if you have PL:Sneak of Shadows active. If your haste IV clicky is active, and you don't have aggro....you soon will.
Since radiance handwraps don't exist, the Bluff skill is your best friend for solo situations. In groups, just let the Barbarian run in first and grab their attention
Assassinate DC would be 23 + Int mod, so probably something like 28-30 at endgame. Not stellar, but might be enough to have some fun in the Vale. Not the main focus of this build, however, and endgame I'd leave Assassinating to the professionals.
Saves would be a base +17/+21/+17 in water stance. With stat mods, these should all be close to or above +30 solo unbuffed.
Throw in Recitation (+2), Greater Heroism (+4), and your clickies (+6 from Uncanny Dodge, +5 from human versatility), and you're laughing.
Stunning Fist DC : 10 + 1/2 char level + WIS mod + any other mods. With an endgame WIS of, say, 30, this DC could be 45+ easily with a +10 stunning item (alchemical handwraps FTW) and eSpare Hand (+5 exceptional bonus). 50+ with a bit more work.
End result is a class combination that is versatile, sturdy, capable of self-healing, does fantastic dps both solo and in a group situation (sneak damage + human versatility damage + haste IV clicky + handwrap speed = zomg!; or stunning fist and +50% base damage from incapacitation if tanking), full trapskills, amazing saves, great AC and damage mitigation (shadow fade), etc.