Update: There is a new and updated version of this post availabe at my photography website:
http://markusjaisphoto.com/cameras/choosing-a-camera-for-bird-photography

Which digital Single Lens Reflex (DSLR) camera is best for bird photography? This is a question many birders who want to get serious about bird photography, are asking themselves.
Today, there are many companies who offer DSLRs, including Nikon, Canon, Sony, Pentax, Olympus and more. The price of the models goes from below 1.000 Euros (or Dollars) up to more than 5.000 Euros for the professional cameras.

Which brand?

That’s an easy question. Canon or Nikon. Period. Although the cameras of other manufacturers are not bad, Canon and Nikon offer the best camers and are the only ones who currently offer professional bodies (Nikon with the D3 and D300, Canon with the 1D Mark III and 1Ds Mark III). In addition Nikon and Canon have the greatest selection of lenses and other useful utilities like extenders.
Canon and Nikon are currently the only companies that offer a 4/500 with image stabilization. Sigma has a 4.5/500, but without stabilization and a much slower AF than the Canon and Nikon lenses. And the Sigma is also available for Nikon and Canon, if you want to use them. The 4/500 is one of the best choices for the serious bird photographer. For more information about lenses, read my post Choosing the best lens for bird photography.
If you are serious about bird photography and want the best equipment currently available, choose either Nikon or Canon.

How many megapixels?

10 megapixels (MP) is the current standard of most consumer cameras and some professional models. Some new models like Nikon’s D300 offer about 12MP and Canon’s 1Ds Mark III even offers about 21 MP.
I think for most cases 10 or 12 MP are enough. If you are also doing a lot of landscape photography, you might want to get a camera with more than 12MP. At the time of this writing, there is only the Canon 1Ds Mark. But more cameras with a higher resolution from both Canon and Nikon are expected to follow soon.

Crop factor or full frame?

Let’s use an example to demonstrate the point why I like a camera with a crop factor. Nikon’s D300 and D3 both have about 12 MP of resolution. The 1.5 crop factor of the D300 will give you the bird with the same size in the image as if the picture were taken with the D3 and a 750 mm (500 x 1.5) lens. That means, when you photograph a bird with a 4/500 with both the D300 and the D3 from the same distance, you will get much more pixels per bird with the D300 than with the D3. That will allow you to make bigger prints.
But keep in mind, that the full frame sensor of the D3 has better image quality. You probably won’t notice this at all up to ISO 400 but above ISO 800, the D3 is the clear winner. That said, the D300 performs very well at high ISO values.

What else is important?

The camera should have a fast and accurate autofocus (AF). Canon and Nikon currently have both very good AF systems. The more expensive the camera, the better the AF. That’s because those cameras have more processing power and a more sophisticated AF system. A Nikon D3 will perform much better than a Nikon D60.
The camera should be able to shoot at least 5 frames per second (fps). That’s important when you are shooting action scenes like fighting birds or birds in flight. A camera with 8 fps will give you a much higher chance to get a good shot than a camera that can only shoot 3 fps.
The camera should have weather sealing, if you will be using it in difficult weather situations like heavy rain, or dusty areas like a dessert or at the ocean shore.
The camera should also deliver good image quality up to ISO 800, which is the case with most current Nikon and Canon cameras.

What do you recommend?

I currently use a Canon EOS 40D and am very happy with that camera. If you want an affordable but great camera for bird photography, the EOS 40D is a great choice. A serious alternative is the Nikon D300. This is a more expensive camera, but also overall a better one. It has a higher resolution than the EOS 40D (12 vs. 10 MP), can shoot 8 instead of 6.5 frames per second, has full weather sealing and a faster and better AF.
If you want to spend even more money, you can get either Nikon’s D3 (12 MP, full frame) or Canon’s 1D Mark III (10 MP and 1.3 Crop factor) or Canon’s 1Ds Mark III (21 MP and full frame).

The lens is more important than the camera

Keep in mind that the lens is more important than the camera. It’s better to bay a Canon EOS 40D with a 4/500 lens than a EOS 1D Mark III with just a 4/300 lens. For more about the right lens, read Choosing the best lens for bird photography

Further reading

Have a look at dpreview.com for detailed reviews of many Canon and Nikon cameras. Another great resource is the review section at fredmiranda.com

Many of the current Nikon and Canon cameras are available the the birdingnet.com shop powered by amazon.com.