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Personally I like to focus manually. For video, autofocus in general is not desirable; and in any case with my lenses, most of them from the 60s and 70s, there's no other option. But the main thing I like about manual focusing is that it makes you work, and think about the image you're about to take: it is the final touch that makes me the one taking the picture, not the camera.
In any case, it is clear that it is not for everybody, or for every occasion (athletes and children move too fast).
If you're going to use autofocus, you have to know a few things about it.
First one: there are two kinds of autofocus:
* phase detect: used by cameras with a mirror ("reflex": SLR, SLT, etc)
* contrast detect: used by mirrorless cameras (compacts, even if they have a big sensor and/or use interchangeable lenses)
Contrast detect is usually slower, and doesn't work well in low light conditions (although it is getting better quite fast).
Phase detect, if it is not well calibrated, will generate systematic errors: unlike contrast detect (which uses the main sensor to focus, and by construction takes lens and camera imperfections into account), phase detect uses separate mini-sensors that have to be placed in a very specific position. But no lens and no camera is perfect: there are error tolerances, and in optical issues often a very small difference can create clearly noticeable issues. If these mini-sensors are farther away or closer, or if the lens is slightly off, the camera will always focus closer (front-focus) or farther away (back-focus) than it should.
This issue is usually small on slow lenses, with great depth of field (f/3.5 or slower), but can be a nightmare at f/1.8 or f/1.4. And it will be more noticeable in tight shots taken with long lenses than in wide shots taken with wide angle lenses.
Mid- and high-end SLR/SLT cameras usually have a microadjustment funcion: place three batteries on a table, each one 5cm closer than the previous one; get the camera a couple of meter from them, and take ten pictures of the battery in the middle; check them and see if this combination of camera+lens front-focuses or back-focuses; tell that to the camera, take another 10 pictures, check them, tell the camera how it is doing, etc., until you're sure the camera is not making sistematic errors (it will still make odd errors, sometimes one way, simetimes the other). Get the next lens on, and repeat. Etc. The camera will remember the microadjustment setting for each lens. In my list of recommended cameras I always try to state if each one has microadjustment or not.
If you're going to buy a camera with phase detect autofocus (SLR or SLT), you have four options:
* get one with microadjustment
* get one without microadjustment and pray
* decide you don't care if focus is perfect or not, and get one without microadjustment
* get the one you like most, and focus manually
For me, the third option is only a good idea if you're not going to use lenses faster than f/3.5.
Much more about these issues in this great blog: here, here, and here.