[edited to add: Most of the information here have been incorporated and improved upon, in the subsequent pages on flash photography techniques.  Specifically, this page discussing the use of  TTL vs TTL BL is more up to date.

However, I'm leaving this page (from 2005) here as a pre-cursor to those more informative pages.]

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Nikon’s flash system is truly superb, making it possible to often achieve excellent results without the photographer really needing to understand the finer workings of flash exposure metering .. but ultimately you will achieve the most consistent restuls if you understand how exposure metering works, as well as having a more clear idea of Nikon’s approach to flash technology.

For instance, you can often get poor or unexpected results if the basic differences in the various TTL modes aren’t understood. The number of TTL modes are confusing, but there are certain similarities which make them easier to understand and use. The manuals for the Speedlights hint at some of the things mentioned on this page, but never discusses outright.

TTL .. vs .. D-TTL and i-TTL
There are some crucial differences between TTL for the film camera bodies, and D-TTL as it applies to Nikon’s digital bodies, but we’ll get to that in a short while. First we’ll go over the similarities ..

Balanced Fill-Flash TTL .. vs .. Standard TTL
The plethora of TTL modes seem confusing, with names like 3-D Multi-Sensor Balanced Fill-Flash, and so on, depending on what camera and lens and flash combination you’re using. (That the terminology is a mouth-ful of words, doesn’t help either.)

There are quite a number of permutations here, whether you use manual focus lenses, or D-series AF lenses, or older AF lenses. It also depends on what series of camera bodies you use, in tandem with which flash series. Every camera model and flash model and lens type interacts differently, and different exposure algorithms come into play.

But here’s the thing .. the various TTL modes can essentially be grouped in two broad categories:

TTL BL / Fill-Flash D-TTL / Fill-flash TTL
In the various Fill-Flash TTL modes, the camera & flash combination will try to keep your flash output as a fill-flash only. It’s important to understand this distinction. This mode is perfect for daylight fill-flash, where the ambient light levels dominate. But as soon as ambient light levels start going down, and the camera in one of the auto-exposure mode keeps the shutter speed around 1/60th (for example), then the camera & flash are still going to try and keep the flash as only a fill-flash .. and hence give less flash output compared to what you’d expect. ie, under-exposure.

Standard TTL / D-TTL
With Standard TTL, the camera & flash combo doesn’t try to balance your flash to the ambient levels. The flash output is considered and measured on its own. (It’s also important to understand this distinction from fill-flash.) Standard TTL is perfect for when your speedlight dominates as a light source .. ie, when you want to take photos with the flashgun as the main light source.

I tend to use the Nikon Speedlights in two specific ways :If I am photographing outside in daylight, and I want the flash as fill-light only, I most often use Fill-Flash TTL. (With the SB-800 this would be TTL BL. With older Speedlights this is where the matrix or daylight symbol appears next to the TTL legend on the Speedlight LCD.) In most cases, it works beautifully just like this, but I still prefer to dial my flash exposure compensation down to around -1.3 or -1.7 stops, while still exposing properly for ambient light. The aim in doing that, is to have the flash barely perciptible in the images.However, if I am photographing indoors where the light from my flashgun is the dominant light source, I find that Standard TTL mode is more consistent and more predictable. (This is where there is no matrix symbol next to the TTL legend on the flashgun LCD.)In Fill-Flash TTL, the camera works according to various algorithms as it tries to figure out how “best” to balance flash with daylight. It does a pretty good job of it, but it is too unpredictable trying to second-guess an algorithm … so it is sometimes easier to just use Standard TTL mode, and if need be, dial in flash exposure compensation to bias your flash exposure up or down.

pre-flashes

Nikon’s TTL flash technology depends on a series of pre-flashes that is emitted right before the actual main flash output. The pre-flashes are used to help in determining the exposure.There are two unfortunate side-effects to these pre-flashes ..There is no way (that I know of), to measure the flash output with a flashmeter to confirm that it is correct. Flashmeters tend to pick up the the pre-flashes and show a reading which is much lower than the flashgun’s actual output.If you optically trigger other flashguns or studio strobes with your Speedlight set to TTL or D-TTL, then the preflashes will trigger the other strobes too early. This means your other strobes won’t register at all on the actual image, leaving your photograph much darker / under-exposed than you anticipated.
Being aware of these two side-effects, can spare you a much frustration later on, so be aware of it.

Also, note that with film TTL flash, the pre-flashes disappear when the flash-head is tilted. However, with D-TTL and i-TTL, the pre-flashes remain for any position of the flashgun’s head.

The preflashes are of very short duration and low intensity, and can’t be distinguished by the naked eye from the actual main flash output .. unless .. you are using a Nikon D70. Somehow with this camera, the preflash bursts are quite noticable and can cause your subjects to blink.

If you do want to see the preflashes distinctly from the main flash burst, then you can set your camera to a slow shutter speed, (say 1 sec), and your Speedlight to Rear Curtain Sync. Then the preflashes will be noticable right at the start of the shutter tripping, and the main flash output will be at the end of the exposure time.

film TTL .. vs .. D-TTL and i-TTL

The big difference between these versionsWith TTL in film cameras, the flash output is measured off the film plane during the actual moment of exposure. But due to the difference in reflectance between film and the digital sensor, Nikon decided this wasn’t feasible, and came up with a work-around to this .. D-TTL.(To Fuji’s credit, they managed to utilise the film TTL flashguns on their digital camera fairly successfully.)As mentioned before, with TTL flash as it applies to film cameras, the flash output is measured off the film plane during exposure, and the actual flash exposure is adjusted during the moment of exposure. The series of pre-flashes are used as a guide to the exposure, but the actual exposure is controlled during the moment of exposure.But with digital TTL (D-TTL and i-TTL), the actual flash exposure is determined (and fixed) before the moment of flash exposure, by the digital camera body measuring the amount of light from the pre-flashes, as reflected off the subject. The flashgun’s output is not adjusted during the moment of exposure.

This has a few side-effects ..

With D-TTL you couldn’t use multiple flashguns in D-TTL mode. Only the single flashgun. This was one of the major improvements with i-TTL which offers wireless flash technology.

Also, if you are shooting in D-TTL or with i-TTL, and trigger other flashguns or strobes by radio slaves (to get around the fact that the pre-flashes will trigger optically slaved strobes too early), you could still run into a problem.

Because the pre-flashes are used to determine the final D-TTL or i-TTL exposure, they don’t take into account the amount of light that your other strobes will emit, because the other strobes aren’t triggered yet, (and would anyway not give the required series of preflashes required to calculate the correct D-TTL or i-TTL exposure). This invariably results in over-exposed flash photographs if the other flashguns or strobes are set to emit strong enough light to register as another main light source. If you use other strobes to to lift the ambient light levels slightly (for example in a hall), then this might not be much of a problem. But be aware of these implications.

Flash exposure compensation is a subject that somehow mystifies a lot of photograpers. This isn’t specifically about Nikon’s flash system, but I noticed on the various photography forums that many new camera owners are confused by the difference between overall exposure compensation and flash exposure compensation.The difference is in how the ambient vs flash exposures are affected, and isn’t all that complex once you understand how ambient exposure and flash exposure tie in to each other …

rear / front curtain syncMy advice is to use front curtain sync. Unless you have a specific reason to use rear sync, it is best to use front curtain sync as your default. With front sync it is easier to anticipate when the motion-freezing flash burts will appear, especially if you are using slow shutter speeds.Another thing I have noticed, is that I tend to get more photos of people blinking, if I use rear curtain sync. I suspect that people are reacting to the TTL preflashes before the main flash exposure.