I'm learning how to jig fish and was wondering how ya'll would fish them on flooded cypress trees in under 5 ft. of water and also on dead trees in about 6-8 ft. of water?  

Also, what color jig would you use?  The water is stained.   What color would ya'll use on cloudy days and what color on clear days?

Same way I fish anything else; Flip-N-Pitch or Cast-N-Hop a Black-N-Blue Jig  

yea black and blue for sure but when u hop it  dont hop it fast because even a jig will snag  i like throwing into the try letting it sink   shake it alittle and pull out very slowly

Definatly black n blue and maybe a little purple added in for contrast. Make sure you get a jig with a decent weed guard and fan it out a little to keep from getting snagged as often. I agree with the flip and pitch and let it sink and then just raise it back out of the tree slowly banging it off of every limb you come in contact with. In this situation you can get away with a heavy braided line to get those fish out easier and faster once you hook up.

Harshman

black and blue jig with a black chunk or blue chunk for the murkey water. clearer water go with watermelon with some zoom watermelon chunks.

Mostly black and blue, but green & brown works pretty good in stained water up here.  As for jigging laydown trees, I pitch around the outer edges then slowly move my rowboat right up against the tree so that I came vertical fish my jigs down. Makes a big difference in how many times one gets hung up and looses a jig. I can also apply a lot more action to the jig before reeling it in.

The jig color question have already been answered so....

For standing timber, pitch to within about 6 inches of it, let it fall to the base, then shake it once it is down there. Make a couple pitches to each, then move on to the next.

For deadfalls, pitch to the outer parts first, especially where the limbs make a V. When it hits the bottom, wait a few seconds, then shake the jig and begin hopping it out. Make multiple pitches and work your way from the front of the tree to the bank.