Rogue 2/Ninja 2/Soulknife 1, or Rogue 2/Ninja 1/Soulknife 2.
Seriously. Advance primarily as a ninja (Complete Adventurer) or soulknife (Expanded Psionics Handbook, or just look at the 3.5 SRD's psionic section), dabbling just a bit in the other and rogue. Your 1st and 5th levels would be in rogue, then you'd just advance your rogue level every once in a while for that extra bit of Sneak Attack and a dumping of ranks into Search/Disable Device/Open Lock (most other class levels will see you spending points on Hide/Move Silently and other skills, not trap/lock stuff).
You'll be sneaky-sneaky, disappearing mysteriously sometimes and then reappearing with you shimmering, blood-red Mindblade protruding from an enemy's throat, only to wink out as you draw and hurl a barrage of shuriken (or another Mindblade) at the next foe. You'll have both Sneak Attack and Sudden Strike, as well as a few tricks with your Mindblade later.
Of course, you'll have to play a Human, Halfling, or Xeph (Xephs from the XPH have Soulknife as a favored class), depending on if you emphasize the ninja class primarily or the soulknife class primarily. By 10th-level you might be a Rogue 3/Ninja 5/Soulknife 2, or Rogue 3/Ninja 2/Soulknife 5, or Rogue 3/Ninja 4/Soulknife 3, or whatever. By 15th you may be a Rogue 5/Ninja 6/Soulknife 4, or Rogue 4/Ninja 3/Soulknife 8, or whatever. At some point, a Soulknife-oriented prestige class from Complete Psion might beckon, or not.
Go for a total of 6, 8, or 10 Soulknife levels (6 or 8 probably best), 3 or 5 Rogue levels (5 probably best for being effective with traps/locks), and 5-11 Ninja levels, by your 20th character level. 4 levels of Soulknife are probably needed early on, to get the +1 mindblade enhancement (to bypass DR X/magic and at least have some chance of harming shadows/wraiths/etc.). Rogue levels are just for taking once in a while (once every 4-5 character levels) for boosting the roguish skills you just need to fill the basic Rogue role of trap/lock remover.
Speed of Thought at 6th-level Soulknife will make you quicker, and if your race is Xeph, you'll have their Burst of Speed ability too for really-quick escape or closing into melee reach in a snap (and make the most of your Ninja abilities to go invisible or whatnot for a single round at a time; invis, charge 80 or 100 or 120 feet, stabbity doom with sneak attack added to sudden strike added to psychic strike, reappear). The Aligned Attack psionic feat could be taken later to do a bit more damage and ignore some creatures' aligned DR momentarily. The Ghost Attack psionic feat will also help, giving Ghost Touch to your weapons usually. Up The Walls is a neat psionic feat for maneuvering ninja/wuxia-style in a dungeon or city environment. Mental Leap may be useful for big wuxia-style jumps, especially with the extra speed you'll have already on running jumps, but ML isn't very great, sadly (only +10 on the Jump check for expending psionic focus). Psionic Meditation may be useful if you end up using Aligned Attack or Mental Leap frequently.
I'm not so familiar with Complete Adventurer, so I'm not sure what level of Ninja is best to aim for, or what prestige classes might best suit a Ninja.
Or at least go Rogue/Ninja (with maybe a brief dip into 1 or 2 levels of Monk or Scout). Less cool than a tricky psionic ninja assassin with blades of physically-manifest spite, but a ninja assassin is a ninja assassin.
