The problems I encounter in photographing my tanks are:  

Reflection of Flash:  A big glass tank is really good at reflecting flashes. If I turn the flash off I get blurred pictures even using a tripod.

Darkness:  When I do manage to get a picture that doesnt have a huge flash reflection in it the tank appears to be unnaturally dark.  My tank is very well lit yet it doesn't show on film.  Perhaps this is because of the black gravel and black background I'm using on it?

Blurred Pictures:  The only way I've found to address the two above problems is to turn off the flash on the camera.  This of course increases the time the shutter is open. However as we all know, fish don't sit still to be photographed.  The combined effects of the heavy plantings swaying in the flow of the water, the bubble wall that circulates water around the heater, and all the moving fish cause the entire picture to be blurred almost beyond recognition.