I like to use a hi-viz braided line for jig & float fishing. Its MUCH easier to see in the water and the braided line floats really well compared to mono. I use a floro leader below the float, I don't believe the hi-viz line is an issue in most situations.
Suggestions I've heard if you are concerned include: using a sharpie to blacken the first ten feet above the swivel or tie on a 10' piece of dark braided line above the swivel or use a longer leader below the swivel. All these would work fine I suppose, but I have not felt it was necessary yet.
As for fly fishing applications, again I think the situation might dictate. Low, clear water? Then maybe a darker line or longer leader to get the fly farther away from the line. If you use your line as a strike indicator rather than a float type strike indicator when nymphing then the brighter line colors might make life easier when trying to detect that subtle take, or so I would guess. I personally use an actual strike indicator as I feel its easier.