I've always shot in aperture priority mode for flight photography. By setting an aperture of f/8, I can get enough depth of field for most flight shots. Most of the time aperture priority works fine, but in some cases I am frustrated by the results. Take these shots of a Black-bellied Whistling-Duck at Green Cay:

Figure 1. Aperture Priority, 1/640s, f/8, ISO 200, Evaluative Metering.

Figure 2. Aperture Priority, 1/125s, f/8, ISO 200, Evaluative Metering.

Both Figure 1 and Figure 2 are of the same duck at the same pass. The camera was set on Aperture Priority (Av) at f/8 and ISO 200. In Figure 1 the camera does a good job of setting the exposure. Figure 2, however, has several issues. First of all the shutter speed has dropped too low to 1/125s due to the change in the colors of the background. Second, the highlights are completely blown at these exposure settings. It will take heavy post processing to get Figure 2 to match Figure 1 in tone and clarity.

The solution is to shoot in manual exposure mode (M). Set your camera's manual exposure settings to the equivalent of the Sunny f/16 rule. Alternatively you can just meter off the blue sky and set your camera to expose it correctly. For me on a bright sunny day this usually comes down to f/8, 1/800s, at ISO 200. Here's a chart that I use for my 20D:

The aperture runs down the left side and the ISO is listed across the top. The shutter speeds are listed in the table. So if you want to shoot at ISO 200 at f/8 we look down the column labeled 200 until we find a shutter speed corresponding to to f/8, which is 1/800s.

So now another Black-bellied Whistling-Duck pass. Again Figure 3 and Figure 4 show the same duck in both images during the same pass. This time shot using manual exposure (M) and the Sunny f/16 rule:

Figure 3. Manual Exposure, 1/800s, f/8, ISO 200.

Figure 4. Manual Exposure, 1/800s, f/8, ISO 200.

As you can see, regardless of the background the images are both properly exposed. Better yet, the shutter speed didn't drop, so motion blur is kept to a minimum and the highlights aren't blown.

There are two disadvantages to using manual exposure. The first is that if your subject is not middle toned and you normally have to dial in exposure compensation, you now have to calculate those values manually. The second is that if the lighting conditions are constantly changing, like on partly cloudy days, you will have to remember to adjust your settings accordingly between bursts of shots.