Dragon Magazine Loves Ninjas
Jackinthegreen found quite a lot of useful Dragon Magazine material for the Ninja
CA. Rather than paraphrasing him, I think I'll just let this gold miner speak for himself
Dragon Mag 342:
Benefits are mostly paraphrased.
Hidden Kingdom Jutsu:
Prereq: Ghost Strike (8th level)
Benefit: Spend ki power to make an effect similar to hallucinatory terrain, but only affecting a 40 foot radius from you and lasting one level. Can expend additional uses of ki power to add +2 rounds per ki use spent.
This might see use by confusing your opponents during a battle, but as with almost all illusions your DM will have to be open to working with it. See if you can get circumstance bonuses to various skills or even total concealment from being within the illusory terrain that looks solid.
Jutsu Focus:
Prereqs: At least two ki feats.
Benefit: Add +2 to the save of your jutsu and if it lets you spend more ki on it to increase its effectiveness you may automatically treat it as if you had spent an extra use of ki.
If you�re investing heavily into the jutsu feats, this will probably be mandatory.
Rabbit Prince Jutsu:
Prereqs: Ghost step (invisibility) (2nd level)
Benefit: Spend a use of ki to move under the effects of expeditious retreat for 1 round. While under this effect your jump distance isn�t limited by your height.
If you need to move fast, this might work for you. The part about jumps being limited by height is actually not in 3.5 rules, but if your DM is restricting jumps based on height like 3.0 did then this is a boon.
Ringing Fist Jutsu:
Prereqs: Ki dodge (6th)
Benefit: Expend a use of ki to apply the effects of a knock or targeted shatter spell on any successful unarmed attack you make against an object.
In short, you punch things and they go boom or open up, whichever you feel like happening. Combos somewhat with the Ascetic Stalker feat.
River Eel Jutsu:
Prereqs: Ki dodge (6th)
Benefit: Spend a daily use of your ki to move as if under the effects of a freedom of movement spell for one round.
This one is actually pretty darn good. Remember that jutsu are extraordinary unless otherwise noted, and an extraordinary freedom of movement is just what the ninja ordered for many occasions.
Shadow Puppet Jutsu:
Prereqs: Ki dodge (6th)
Benefit: Spend a daily use to force an opponent within 30 feet to make a Will save. If it fails, it is flat-footed until the beginning of its next turn. This is a mind-affecting effect.
Useful to set up Sudden Strike damage.
Thousand Faces Jutsu
Prereqs: Ghost Step (invisible) (2nd)
Benefit: Spend a ki use to be affected as if by Alter Self for one minute, but you can only change into a creature of your size and type, and you gain none of the movement or combat benefits of the new form. Spend two ki uses to assume the form of a specific creature of your type for a minute.
Looks more like Disguise Self to me. If you�re really into this sort of thing, the Changeling race is probably a much better fit.
Wind Oxen Jutsu:
Prereqs: Ghost strike (8th)
Benefit: Make a special bull rush attack on an adjacent target with a bonus equal to your Wisdom mod + � your ninja class level and can expend additional ki to add +4 per use spent. There�s no need to actually touch the target, and this ability does not provoke an attack of opportunity.
Bull rushes have plenty of fun uses, but the bonus on this leaves something to be desired. By the time you get this, your bonus should be at least +7 (4 from ninja levels and +3 from Wis mod), which is the mod the fighter could have had from 1st level (16 Str and Imp Bull Rush). Don�t expect to push around much unless you spend a lot of ki on it.
Dragon 351
Karmic Healing
Prereqs: Ki power (1st)
Benefit: You can spend a daily use of ki to heal yourself a number of hit points equal to half your ninja level (minimum 1) times your Wis bonus, or spend a use to remove the fatigue condition or reduce exhausted to fatigued.
If you�re pumping wisdom, this might actually be pretty good once you have several ninja levels. At 10th a single use could get you 25 HP.
Ki Smite
Prereqs: Ki power, Sudden Strike +2d6 (3rd)
Benefit: Spend a ki use to add your Wis mod to your next melee attack roll and your ninja level plus your current ki pool (not including the one you just spent to get the smite) to damage.
Another good one if you�re pumping Wisdom and ki uses. Note that it doesn�t say the damage only applies to hit point damage, but it�s safe to say the designers intended it to only work on weapon damage and not ability damage for instance. Abuse at your own risk.
Skill Attunement
Prereqs: Wis 13, ki power (ghost strike) (8th)
Benefit: You can spend a daily use of ki to grant yourself a bonus on all skill checks equal to your Wisdom bonus for a number of rounds equal to 1/5th your ninja level (rounded down, minimum 1).
Very useful when you want that extra oomph to your skills.
Wolf�s Bite
Prereqs: Ki power (1st)
Benefit: You can spend one daily use of ki to gain access to Improved Disarm, Improved Feint, and Improved Trip for 1 round.
This allows you to be more versatile as needed and without having to spend the prerequisite feats. Not bad.
General feats:
Intuitive Trapsmith
Prereq: Ki power
Benefit: Add your Wisdom bonus instead of your Intelligence bonus on all Search and Disable Device checks. These effects are always active.
Chances are your Wis is higher than your Int. This will allow you to eke out a bit more from those skills and help you function better as a trap handler, though the ninja really isn�t the best at that role.
One With Earth and Water
Prereq: Ki power (1st)
Benefit: Add your Wisdom bonus on all climb and swim checks instead of your strength bonus. These effects are always active.
Bit of a shame it doesn�t apply to jump checks too, but if you see yourself using these skills regularly then they help make you more SAD. If you want to totally ignore strength-based skills, the feat Agile Athlete makes your climb and jump checks key off dex instead.
Zen Fortitude
Prereqs: Ki power (1st)
Benefit: Add your Wisdom bonus (instead of your Constitution bonus) on Fortitude saves. This effect is always active.
Another feat to make you more SAD. Just make sure not to skimp on Con because more hit points tend to be quite helpful.
Here are some multiclass feats the CA ninja technically qualifies for, and the Rokugan ninja definitely qualifies for but technically doesn�t gain the benefit.
Daring Outlaw:
Prereqs: Grace +1, Sneak Attack +2d6
Benefit: Stack swashbuckler and rogue levels to determine SA damage, Grace progression, and Dodge progression.
If your DM allows you to progress the class that gave you Sneak Attack/Sudden Strike with this, then it�s probably worthwhile. The later levels in both CA and Rokugan ninja aren�t really worth much. For the price of a feat, you get another feat you�d probably have taken anyway (Weapon Finesse), a bonus on reflex saves that will probably be overwritten by buffs since it�s a competence bonus, and a bonus to AC that is better than dodge except it doesn�t count as the feat for prerequisites like the Rokugan nina�s Ninja Dodge does. Taking a third level in swashbuckler gets you Insightful Strike which will give you some extra damage but likely not much if you�re not focusing on Int.
Ascetic Rogue:
Prereqs: Improved Unarmed Strike, sneak attack
Benefit: Add 2 to the DC of your Stunning Fist attempt if it�s also a sneak attack delivered with an unarmed strike. Stack monk and rogue levels to determine your unarmed strike damage.
The unarmed strike progression is helpful. The Stunning Fist stuff may or may not be since the feat is fairly weak on its own without specializing. I wouldn�t recommend this feat unless you really know what you�re doing.
Between all those feats, I'd be inclined to promote the CA ninja to Tier 4 due to the increased versatility and power.