I've heard many different methods, but the one I use is the alphabet. For each 50 I do it's one letter and I say all the things I can think of with that letter (apple, angel, angry, animals, abacus, then the next 50 is bears, babies, bubble gum, bumblebees etc). I know if I got to the letter H it's 400, if I get to Z it's 1300. Easy for me to keep track of.
My DH just counts in his head for each 50 (says over and over for each 50; 1,1,1,1,1, then the next one is 2,2,2,2,2, etc).
They also make really cool counters that go on your finger and for each lap you tap it with your thumb and it keeps track. Those cost about $30 and I'm cheap so I use the alphabet (it's free).
http://www.sportcount.com/products.php