That was a comprehensive and excellent explanation of DOF and hyper-focal distance.
There are three general ways that I will focus:
1. Focus on the subject... when the specific subject is the most important portion of the image. This is very important when you are using shallow depth of field to isolate your subject: i.e.: having the foreground and most importantly the background blurred out of focus to either bring attention to your subject or eliminate a busy and/or distracting background. (See image of dragonfly) BTW: often the angle of view or positioning of the subject will help you keep that subject in focus. If I had shot the dragonfly head-on, there is no way that I could have kept the entire insect in focus. This is O.K. when you desire just a head shot but, annoying if you desire to show the entire insect. Using a side view, I did not require as deep a depth of field as I would have head-on.
Additionally, you can often blur annoying foreground distractions such as when you are shooting at a zoo through a mesh cage. Using a longer focal length and a wide f/stop and focusing on the animals eyes will often prevent the mesh from being a distraction. Just make sure that your camera is focusing on the animal, not the mesh. (See image of Cheetah cub). I shot this using Aperture Priority exposure with my 70-200mm f/4L IS lens at f/4. If you look closely, you can see evidence of the out-of-focus mesh on the back wall and on the foreground. This is however, IMO, far less annoying than seeing an in-focus mesh barrier between you and your subject. It can, if you desire, be easily corrected using a photo editing program.
In images of people or animals; the eyes are the most important point of focus. As a quick aside; when shooting individual or team sports - I will most often shoot from a low angle and select the top focus point in my camera. That way, the heads or eyes will be the primary point of auto-focus.
2. Focus for best over all depth of field: I use a relatively small f/stop. However, don't like to shoot below f/11 - or at the absolute minimum f/16; because diffraction will degrade the sharpness of the image.
http://scubageek.com/articles/diffraction.pdf
I will also generally focus 1/3 into the important portion of my image. Depth of field is greater to the rear of the point focused on than it is to the front.
Canon includes an A-DEP mode on their xxD DSLR cameras (I don't know about other models or makers). This is supposed to select a focus point which will give the widest depth of field or keep the major portions of your image in focus. I don't use any of the camera controlled shooting modes because I like to control my own imagery.
3. Finally Using Hyper focal Distance: This is an excellent way to shoot quickly in manual focus. It is especially good for grab shots in the dark - especially outdoors when your autofocus will not work.
Set your manual focus at the hyperfocal distance and you will be in focus from 1/2 that distance to infinity.
Naturally, this requires a lens with a focus scale. Manufacturers, aiming for lower prices, have eliminated focus scales from many autofocus lenses. The Canon 50mm f/1.8 Mark-II is an example. The original Mark-I model had a focus scale but, it was removed from the Mark-II model.
Older manual focus lenses often had a scale which included two sets of f/stops engraved, one set to either side of the focus point. That was a quick and dirty way to determine what your depth of field was. You would be in focus from the f/stop you are using on one side of the focus point to the f/stop engraved on the other side. This was a wonderful way to achieve quick focus in the days before auto-focus cameras.