Because this is a common question and most of us agree this is the correct procedure, I am outlining the basics of how to flush the A4LD, 4R44E, and other similar A4LD derived transmissions. This method is safe and will not harm the transmission, can be done in your own back yard, and can extend the life of the transmission.

Depending on how the vehicle is used, this procedure should be repeated every 20,000 - 30,000 miles. If the fluid gets older than that, it begins to break down, and also gets saturated with burnt friction material, which is too small to be removed by the filters, and gives the fluid a darkened color.

You will need:
• 12 Quarts of Mercon III or better fluid. Mercon V is preferable, as are synthetic fluids
• A short section of 3/8" ID tubing, preferably clear so that you can see the fluid in the tube
• A bucket or tray large enough to hold 12 quarts (3 gallons/11.3 liters) of fluid
• A gooseneck funnel for adding new fluid through the dipstick tube
• A new filter set with a neoprene gasket
• The regular tools, specifically screwdrivers and/or pliers to remove clamps, sockets or wrenches to remove the transmission pan, etc.
• Some kind of rack or stands to raise the vehicle for extra ground clearance. While not a requirement, it can make the job easier
• A helper to turn the engine on and off and to just help in general
• Transmission modulator (optional and only applies to the A4LD, the newer models use electronic modulators)

1: Place your bucket or tray beneath the transmission. Remove the bolts holding the pan in place, being careful not to drop them in the bucket. You do not have to fully release the pan to drain the fluid. If you have installed a drain plug kit, it can make draining much of the old fluid easier and less messy.
2: Once the fluid is drained out, remove the pan and replace the filter. Look closely at the types of materials trapped in it. It is normal to find lots of small particles, but metallic flakes could indicate the early signs of a major component failure. The amount of material will vary with the age of the transmission as well as the frequency of the changes. Also check the pan for material before you clean it off.
3: Now is a good time to replace the transmission modulator if applicable. The modulator is located in a location where it is exposed to high temperatures. The heat makes the rubber parts inside brittle and can cause this part to rupture. I make a point of replacing mine at least every other fluid change.
4: Install the new gasket and replace the pan. Refill the fluid to the proper level.
5: Locate the return line coming from the transmission cooler. In most cases it is the rightmost (the vehicles right) one. Disconnect it and attach your clear tube and route it to your bucket.
6: Have an assistant start the engine. The fluid should begin pumping.
7A: In this method, you let about 2 quarts pump out, then turn off the engine and add 2 quarts. This is the method I prefer.
7B: Add new fluid as the old fluid drains out. You will likely not be able to add the new fluid at the same rate as the old drains. Shut off the engine if bubbles begin to appear in the outlet tube and allow time for the transmission to refill.
8: Repeat steps 6 and 7 until either you run out of fluid or new fluid begins pumping out the outlet tube. Also some people like to add extra conditioners and additives at the end. I personally don't trust additives, and they are not needed if Mercon V is used.
9: Check the fluid level with the engine running and the vehicle on a flat surface. If it is too low, add fluid until it is the correct level. If it is too high, you will need to drain some out through the return line. Drive the vehicle a short distance and check the level again, to ensure that no air bubbles are trapped or that fluid trapped in the dipstick tube causes a false reading.

And that pretty much covers it.
Of course, there are lots of tricks and techniques you can use to make the job easier and faster. Some people like the pan drain plug, some also like to use a t valve in the return line for draining the fluid instead of disconnecting the line.

If I missed anything or was wrong on any points, someone please jump in and correct me.

Also, could someone pin this?