The Geisha Arguement
The most common arguement I wish to destroy here is the "why have the Ninja if you can have the Geisha?". This is simple, personal preference. It is fun and challenging to have to build a Ninja up from level 0 to a level where he can actually be worth something. Isn't this why we play games to begin with, to have fun and be challenged? Why do you want to race to get one unit, the geisha, then go kill every Daimyo or Heir or even Rank 5 General in the game without any effort? Is that fun? Is that a challenge? No, its about instant gratification and winning. If thats what you want then go play Quake on God Mode. You'll kill everything and you will win. Oh and watch The Terminator while you are at it.

Vs. Shinobi
Another frequently asked question is about the Ninja's spying and counter-spying abilities with respect to Shinobi. Ninja can spy in enemy provinces just like a Shinobi. And I believe strongly that his chances of getting caught are directly related to his honor level just as the Shinobi's is. As for causing discontent in enemy provinces and squashing revolts in your provinces, I have used the Ninja only with Shinobi to accomplish these things. But those roles should be carried out by the Shinobi as their impact on the situation seems to be much more potent.

The counterspying role again seems to be able to be carried out by Ninja as well Shinobi. However, I never deploy a Ninja to do this speific job. I may have him in a territory with Shinobi and I do notice a difference in the counterspying "groups" ability to catch enemy infiltrators.

The main thing to point out here is that a Ninja's honor only goes up when he kills succesfully. Although he can perform the duties of the Shinobi to a lesser degree, his honor will not increase as the Shinobi's does. So the Ninja makes a good backup for your Shinobi when he is not out killing anyone.

What to Watch Out For
The first thing to learn is that Ninja are going to die no matter how good and careful you are. You may spend alot of time getting that one Ninja to level five and think your set, well you are not, he may die. A group of level 6 Shinobi will easily catch your Ninja and kill him. To combat this make a lot of Ninja and train them all as much as possible. By having alot of them around you ensure at least one or two will make it to the higher levels, but you still must be careful.

Shinobi are a big threat to Ninja, to me they are the biggest threat. You don't know where they are or how many their are around your target. There are ways to avoid this though. The enemy will probably keep the most Shinobi around his important generals, Heirs, and Daimyo! So stay away from them. Its that simple, until your Ninja is advanced enough to avoid detection by these Shinobi it is futile to bother with such targets.

Another big threat to your Ninja is Border Forts. Border Forts act as Shinobi in that province. The exact honor level the Forts work at is unknown to anyone as the developers do not release information on such things. Unlike the Shinobi, the Border Forts are detectable. This is the main reason for having Emissaries around later on in the game. They are the only spy you have that can not be caught by Shinobi or Border Forts themselves. They can be killed by Ninja but if you keep your Emissary moving every turn you can usually get him to his destination before he's killed. Once they have made it to the province you can then see if you are in danger of Fort detection.

The final threat to your Ninja is yourself! Yes, you are one of his biggest threats. Players just want to get him that one more kill so his honor goes up. Its understandable, everyone wants to kill with their Ninja, but its this ambition that makes Ninja die. Patience is one of the three ingredients to making successful Ninja and we all forget that from time to time. So by all means, a 50% chance of killing a target means you are going to die. Don't get greedy.

How to Raise Ninja Honor
Yabusama has compiled these guidelines

1. Try and create your Ninjas early on,and create 3 or 4. Some will fail and die early on, but once you get going they are pretty unstoppable. With your brand new Ninjas surround your Daimyo. In the early stages of the game the AI is alliance mad and it is these Emissaries that will give your Ninjas a foot up the honour ladder.
2. Now your ninjas have some honour head for your nearest ronin province. Ronin very rarely use Shinobi or develop Border Forts so you are safe from detection. With your honour 1 or 2 Ninjas start killing ronin generals. As far as I can ascertain Ninja honour is the same as a Taishos rank. So keep plugging away on those ronin until your Ninjas are 3-4 honour.
3. This is the good bit, scout, with your Emissaries, the enemy provinces looking out for 1) Border Forts and 2) enemy Taishos of rank 1 or 2. If there are no Forts and Generals with rank 1-2 then send in the Ninja. Be careful that your target doesn't leave the province, once assigned a Ninja will follow him until he catches up, and he may just wander into a Border Fort protected province enroute. Killing these rank 1 or 2 Taishos speeds up the rate at which the Ninja gains honour. I don't know how much but the Ninja will certainly speed along. Try not to kill anyone if the chance is below 75%, all that time spent training is too much trouble to waste on a careless attempt.
4. If there are no enemy Taishos to wack, kill ronin. Aim for each of your Ninjas to be killing someone EVERY turn. It doesn't matter if your honour 5 ninja is only killing some ronin nobody, all kills count in the long run.
5. If the campaign is a long one, eventually enemy Geisha will appear. You have 2 options to counter this, your own Geisha or Ninja. To build your own Geisha is expensive and very time consuming, Ninja are cheap and available early on and can kill Geisha very easily. If you suddenly see AI Geisha appear and you have no Ninja, quickly make 3-6 and surround your Diamyo. These honour 1 Ninja can mob and kill any Geisha that lifts her skirts near your main man. The cut scene for the Ninja killing the Geisha is pretty cool too.

The more I play with Ninjas (not in a funny sort of way, you understand) the better they seem. They do not have the Geisha terminator-esque abilties and seem to fit into the feel of STW much better. For a long time I had big problems with getting my Ninja's honour up but after help from Lanza and others on the offical forum I have now developed the knowledge to get a Ninja as high as 7th. Using Ninja as above, and slowly cultivating them on ronin before moving on, I have had great success with them.