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Color isn't that important. What you do need to watch out for is the proper type of silicone. There are two basic types. "Standard silicone is used in making aquariums and is safe for fish. The other type is used in bathroom caulking and contains an anti fungicide that will not do your fish any good.
Making sure you have the right one can be a bit of a pain. Manufacturers tend to claim their product is suitable for all kinds of things when it actually isn't. The best rule of thumb is to look and see if it is labeled safe for aquariums. In general the other stuff will not make this claim.
As an alternative to silicone, have you considered any of the new polymer based mastic now on the market? It tend to adhere to more type of plastic and rubber that silicone won't stay attached to in the long term.
B.Scott
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