Here are my rules of thumb:
1) When bottling a batch, I try to use all the same color/style bottle if possible. It makes it easier to keep them together and identify them in the wine cellar.
2) Dark wines don't really benefit from clear bottles because you can't see through the wine anyway; therefore, I use green, blue, or brown bottles for dark wines. The darker glass also helps protect the color, but this is a minor factor since my cellar is almost always in the dark.
3) Light colored wines look fabulous in the clear bottles.
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