For the main chamber, use a rubbermaid bottle. These work better than any other container that I've tried. They make a bunch of different ones, and you can buy them anywhere. Try Wal-Mart, Dillions, or Kroger.
Most of the lids that they come with have at least one nice hole in them. Go to a hardware store and get a short piece of vinyl hose that will fit tightly into the main hole. This is where you will toke from.
While at the hardware store, you also need to get some copper tubing and brass fittings. The diameter of the tubing will depend on the size of the bottle. A bigger bottle will require larger tubing so that more air can be pulled through it. Generally, 3/8 inch to ½ inch diameter works pretty well.
Now, to make the bowl, you will need two brass fittings sized appropriately for your tubing. You want the flare-type fitting, not the compression type. Most hardware stores will flare the end of the tubing for you, if you ask them. Make sure they only do one end. The first fitting slides over the tubing from the bottom (non flared end). The other piece you need screws into the first piece, and forms your bowl. The flared rim on the top end of the tube is sandwiched between the two fittings, and the whole thing becomes air tight.
You put the screen into the top piece. You now have a perfect bowl, which is easily removable for cleaning.
The next step is to make or enlarge a hole in the lid for the copper pipe. A power drill works pretty well. You simply shove the tube down the hole, and the bowl rests on top. You need to use some hot glue to seal up the area around the bowl, so there aren't any air leaks.
Some of you may think that the best way to make a bong is with the bowl on the side like some commercial bongs, instead of the top like this design. The advantage of having it on top, is your bottle remains totally intact, and therefore won't ever leak. Cutting a hole in the side and sealing it up with silicone is a much sloppier method in my opinion.
Once all of the parts are in place, and sealed with hot glue, you're ready to go. If you want a carb, you can drill another hole in the lid and put a piece of small diameter vinyl tubing in it. If you keep the end of the tube just above the water line, it works perfectly.
One last tip, these bottles easily accept ice cubes in the top. Ice water works much better than room temperature.
Have fun.