Most people usually use brown pry off bottles. Clear and/or green bottles can be used but you have to be careful to keep them out of the light. Using twist offs is an often debated topic here, you can use them but you need a good capper. Aluminum bottles can also be used, though I never have. I don't think they'd have anymore effect on the taste of your homebrew than they have on the beer that was in them originally(which is basically no effect at all)
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