I agree with whats being said and to answer your question, I would rather see the fly line on trout streams so I can better control the drift of the line and avoid the aforementioned unnatural movements and ripple patterns. If your still concerned with the color, give the new zealand grey a shot- you can still see the line well but it supposedly blends into the surroundings better from a fisheyes perspective. I have noticed a slight difference in spooking ratios in some spots using the new zealand grey color. Or I might have been more sober at that moment in time than in others. Who remembers?
I recently went to the Bahamas and threw a Rio fly line with an intermediate type I sinking tip that I really loved. The tip is 15' and is clear, while the rest of the line is tan in color. I only fished it for one day but it cut through the wind a lot easier and gave me some extra confidence about not spooking the fish. Especially when my high quality casts slapped a cruising bonefish or two on the dome. I thought the comments about fishing clear lines in the salt were very insightful and I can definitely see bigger advantages in the salt with a clear line where its not as crucial to see your fly line or get a precise "drift".
Spent all morning surfing the net for the camo lines but couldn't find them. Where dey at!!?