One of the main causes of stopped up drains in our area is algae growth in the drain line. Algae is formed because dirt and dust that accumulates on the evaporator coil gets washed down the drain line. This combined with the cold water standing in areas of the drain can cause algae to grow. Two things to do to minimize the potential for algae growth in your drain line are to use a good high efficiency filter to keep the dirt and dust off the coil and to treat your drain line periodically.
To treat you drain we used to recommend pouring diluted bleach water through the drain system to kill the algae. You can also use vinegar because it it much less corrosive and will kill the algae just as well. This treatment should normally be done two or three times per cooling season.
To treat your drain line you should first turn your system off so that the blower is not running. Then you should have an access fitting to be able to pour about 1/4 cup of vinegar down the drain line. If you have a trap in the drain make sure it goes into the trap for best results. Let the vinegar sit in the drain line for about 5 minutes then flush the drain line by pouring about a gallon of water through it. Doing this at least once per cooling season should minimize the chance of an algae build up clogging your drain line.