When choosing a fly for fly fishing you must consider several factors. As you progress, you will find several flies that work best for you in your particular environment and season. You will develop favorites and harbor an illogical dislike for others. Sometimes, choosing a fly is about what your gut tells you. But here are some guidelines to get you started.
When choosing a fly for small or largemouth bass in shallow water consider flies that emulate bugs, small prey fish or frogs. Black Bass dwell just below the water line so surface flies like a Chewy Pop or a Mega Whammy are safe and effective choices.
If your target is bass in deeper water, below 4', get your hands on a fly that is made to go low. Some good ones are the Baby Bass Popper, the Bobbie Frog, or the Fire Tiger.
Then, sometimes, you're after those tasty treats, like Sunfish or Crappie, that fit nicely into your frying pan. The #14 Gold Ribbed Hare's Ear is a standard that you will find in any fly shop or box store. But, poppers and bushy dry flies are important to your stock as well. Nudging schooling Crappie around a pond is tons of fun and can be done with cork poppers, wooley buggers, and nymphs.
Pike and Pickerel are hunters, assassins, lurkers, pouncing on whatever floats by. Brightly colored and moving flies like the Mickey Finn stremaer or the Dahlberg Diver will make you successful. Be sure to choose a fly that is the same size as their prey at that time and fish along interruptions, natural or otherwise, of the coastline.
Choosing a fly for trout is on another level entirely, but worth the effort. Trout will respond to what is hatching in their environment at the time, so ask around. Know your trout's universe. Stone flies, caddis flies, and mayflies are your best options. And find out when the yellow mayflies will hatch, then get to the creek and use a #16 Parachute Sulphur.
Choosing a fly for fishing is part of the fun. Practice. Experiment. Hang around your local fly fishing retail outlet and ask questions. Everyone there has a secret fly, a super secret spot (which you will never find) and a double secret fly (which they will tell you about because, after all, they are the experts). Soon, you will be the guy answering questions with that knowing look in your eye.