As a general rule, silicone is color coded for charicteristics. For instance, red is high temp, blue is muti purpose, clear is an adhesive, black is oil resistant etc. Hardware store silicones are colored for asthetic purposes, As a rule clear is usually the only pure silicone, and many of the clear silicones have anti-mildew additives as mentioned. I recently bought a new tank that had a transparent black (more of a charcoal grey) silicone on it so someone is making a black aquarium silicone now. Since the clear is the best adhesive as a rule and also the purest, It would be my reccomendation, if you do chose a colored silicone, read the label carefully if it doesn't list aquariums under uses, don't use it. the additives will cause much gnashing of teeth later on.
Dave