Everybody likes fungus on the deck! Oh wait, no one likes fungus on the deck -- or mildew stains, dirt or weather-beaten patches.
It's tempting to just bleach the whole thing will-nilly, but don't give in. Pressure wash the deck and -- this is easy enough -- use an actual deck-cleaner solution.
When you're done with all the washing, it's time to restain. There are finishes and colors a-plenty, so you should be able to find whatever it is your heart desires. Look for something with a protective finish to repel water (and UV rays).