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What is the difference between using a motor on the camera body and the motor built into lenses?
Aside from how both compare in terms of speed, what differences would I notice if I use a body with a motor and motor-less lens, and a lens with motor on a body that lacked one?
A comparison chart outlining the various lens motor types would be a great help as high end USM motors for Sigma lenses are faster then their regular versions.
Sometimes the AF motor in a lens is a screw and gear type, and in that case it's really not much different to an in-body motor except that it actually has the disadvantage of being more bulky. This is the case on many lower cost lenses (including many kit lenses).
At other times the AF motor in a lens is of the ultrasonic motor type, which uses direct drive, requiring no gears and is superior to a screw and gear type used in camera bodies for several reasons:
The Wikipedia page on the ultrasonic motor (which was apparently pioneered by Canon) is quite interesting and has diagrams.
As mattdm has helpfully pointed out in the comments, some newer screw and gear type autofocus drives are being marketed by Canon as "Micro USM". This is, in my opinion, deceptive. These still have gears so they don't have the advantages listed above.
A lens motor in your camera body only adds a small amount of bulk, and means that your lens selection is a little better and you can AF with some of the cheaper lenses. If you think you'll be served fine by lenses with in-built motors, it doesn't matter so much whether you have it in the body. Obviously, the ultrasonic motor or SWM lenses are the better technology and these don't depend on a lens motor in the body.
As has been answered before, if both your camera body and lens have an AF motor, the lens one is used. And that's the way you'd normally want it because these are usually superior.
This is not an issue with Canon, who do not produce in-body autofocus motors.
Honestly, whenever you are comparing entire categories of things (are pancakes better than waffles?) there is little chance of finding an answer.
From my observations, having the in-body focus motor means that most of your lenses move at more-or-less the same speed. The time it takes to determine focus though will normally vary according to the maximum aperture of the lens though. Even when buying a third-part lens, the focusing speed stays more or less constant between lenses with the same maximum aperture. It is possible that upgrading your camera makes all your lenses focus faster.
Having the in-lens focus motor means each lens has its own focusing speed. I found that third-party lenses, even ones with great optical quality, often skimp on the focus-motor and move noticeably slower than the brand name ones. Focusing speed is much more likely to vary between lenses. Some very cheap plastic-mount kit-lenses are extremely slow (like the 18-55mm that comes with the Nikon D3100). To improve AF speed you will have to do it one lens at a time.
I do agree with @Imre and that in-body focus motors are usually louder but there are exceptions. Some non-supersonic in-lens motors are loud.
I agree with this is a small sample but with about 40 or so DSLRs, I have never seen an in-camera focus motor fail. With a similar number of lenses, I have seen 2 in-lens focus motor fail. Maybe the motors that one can fit in a lens are more fragile?
For me, the most noticeable difference is the louder acoustic noise during focusing when using body motor because
That noise might catch the subject's attention before getting a picture of them acting natural or scare away the animal you are trying to photograph. As a workaround, manual focus could be used in such situations.
Body motor is a cheaper design because you won't need to hide a motor in every lens.
As I recently learned, there's an exotic tele-zoom Sigma 200-500 f/2.8, a huge beast, where the glass is so heavy that an in-lens motor with a dedicated in-lens battery is used even during manual focusing. I suspect most body motors would burn themselves trying to push those glass walls around.
From my limited experience, the in-lens motor pros tend to speed and sound.
However, there is one con that I haven't seen mentioned yet, and that's if you use an extender or other device between the camera and lens. Depending on the in-lens focusing system, it's quite possible that it will continue to focus as if it's mounted directly on the camera body, so autofocus will be completely out of focus. In that case, you have to either manually focus, pick a lens that uses the camera body motor, or do without the extender.
