Throughout most of the year I recommend using a white colored strike indicator when nymphing deep runs and pools (if, of course, bobbers are your bag). The idea is for the indicator to blend in with the foam and not spook fish. This strategy works so long as you can still identify what is your indicator!
This time of year there can be a lot of light brown and bright yellow leaves drifting down stream and congregating in back eddys. If you have a tendency to use white or yellow strike indicators...you could be in for a long and frustrating day. Be sure to have some really gaudy bobbers. They may be the only thing to stand out on the water.