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Strength Base your ninja, because it pays off more if you want to focus on in combat stuff.
Weapon Focus, max weapon enchant as much as you can, try to go for power attack+Furious Focus on strength builds, or dip urban barbarian for dex builds.
Multiclass a level of full BAB class. You will get +1 attack and either rage (+2 attack and 2-3 damage), a feat (weapon focus), favored enemy (+2 attack, damage), smite evil, challenge, or other.
Pressure Points ninja trick for dex damage with hits to lower AC. Its the same as raising attack bonus, but the rest of the party feels it.
Reflavor alchemist/bard/inquisitor as a ninja :)
a small group of bonus-adding things by mattastrophic from the 'let's make the rogue work' thread--most of these apply to ninja's as well:
-Weapon Finesse, possibly through the Finesse Rogue talent. This feat enables a Rogue to focus on Dexterity and not have to worry about boosting Strength. Of course, there is the damage issue due to having less Strength, an issue which can be somewhat alleviated with things like the Dervish Dance feat, an agile weapon, and Sneak Attack.
-Weapon Focus, perhaps through the Weapon Training talent. This one's pretty obvious, though it can get a bit tricky when using it with certain two-weapon fighting builds. It's more desirable to dual-wield two of the same weapon with this feat, meaning that, for example, kukri/kukri becomes more desirable when compared to rapier/kukri.
-The heroism spell. This spell adds to attack rolls, skill checks, and saves, all of which the Rogue enjoys. It also lasts a really long time, meaning that a Rogue can get a lot of mileage out of scrolls and potions. This is a great spell to ask your teammates for.
-The courageous weapon enhancement. This enchantment boosts the bonus provided by morale effects, particularly heroism.
-The Gang Up feat. The effectiveness of this feat for achieving flank (and thus +2 to attack rolls) is very dependent on the Rogue's party. Since the Rogue gets so much benefit from flanking his target, this feat is definitely worth considering. In my experience, its usefulness tends to drop off in later levels, once hasted full-attacks become very lethal and full-attacks with enough allies threatening the target become rare. Things just die too quickly for Gang Up to work in the later levels.
-The menacing weapon enhancement on an off-hand weapon or an amulet of mighty fists. A situational +2 to hit is not worth a +1 weapon enhancement on a primary weapon, but it pulls double-duty when on an offhand weapon or amulet, since the bonus applies to attack rolls beyond ones made with the menacing weapon itself. Combines well with Gang Up. Also note the adjacency requirement.
-The Militia trait from Dragon Empires Primer. +1 to hit when flanking.
-The Outflank feat. This one requires a teammate to take it as well, but is very strong for a Rogue when a teammate has it. It also gives a Rogue a reason to wield a weapon with a large critical threat range, like a rapier or kukri, as doing so increases the chances of granting the teammate a free attack. I'll have to look into whether it combines well with Butterfly's Sting from Faiths of Purity.
-A bane baldric. This is a very strong item for Rogues, because its ability to provide +2 to hit as a swift action is very useful, on top of the extra 2d6+2 damage. It's a great buy at 10,000gp. Note that unless the wearer has Inquisitor levels, it only works with light or one-handed weapons, weapons which fit a Dex-based Rogue's weapons of choice.
It's worth noting that activating a bane baldric requires a swift action. So do many of the Ninja's ki powers. Since the wearer cannot use more than one swift action per round, this means that the Ninja's ability to spend ki for an extra attack conflicts with the powers of the bane baldric, reducing the extra attack's usefulness as a go-to ability in every full-attack.
-Boots of speed. Not only do they give a +1 bonus to attack rolls, not only do they grant an extra attack in a full-attack, but they also increase the Rogue's movement speed, enabling him to move into a flanking position or other ideal attack position more easily.