For clear water, natural colors work best. Use colors and sizes according to forage that time of year. For instance, in fall, the shad are pretty large. A 3/8 oz. white spinnerbait works great. For worms, green pumpkin and watermelon (watermelonseed) work awesome. Motoroil is also good. I also like to use chartreuse and junebug in clear water (although they are considered muddy water baits).
In muddy water, darker lures or bright lures work well. Try junebug, or chartreuse. A dull color like bonewhite also works tremendously. Black, and black/blue flake are also top of the list. For hardbaits, fire tiger and bone white are great producers. Soft plastics, junebug, black, black/blue flake, and chartreuse work great. For spinnerbaits, chartreuse, chart/white (for slighty stained or clear water), or where you can find them, firetiger spinnerbaits work best. Use large, round blades to make a lot of water displacement so it makes it easier to find in muddy water. Also, copper blades and painted blades work much better than silver or chrome blades. Hammered blades can also let out more light.
Experiment with different colors, to find what color works best for you.