I fish primarily in a lake that has Crystal Clear water (actually by definition, you can see a white tube deeper than 8ft down, think Tobermory) and I have dark green braid as a mainline on my baitcasting gear, and bright red braid on my spinning gear using a flouro leader for both. I used to buy line that I thought matched the water colour, and light penetration, but I've don't think that it really matters in the slightest as long as you've got the flouro leader. If I can catch fish on lines that are dark green and brown, or bright red or pink or fluorescent green in a lake that clear, I can catch on any line. I just switch out the weight of my leader now depending on the species i'm targeting.
Now I go for the ones I think look cool! Love that bright red Power Pro =D looks awesome with my all white spinning outfit.