well for me, a square to the tank, normal pic with flash is out of the question, i always get something like this...
so what i have figured out thru trial and error...
use a tripod (stability)
use high ISO, and generally i also use the close-up function(as marcus stated, faster shutter, less chance of a blurry pic because the fish doesnt get as much time to move when the actual pic is taken)
use alot of extra lighting, your flash on the camera itself will likely just make a bad photo (thank you glass reflections)
ANGLE YOUR CAMERA TO THE GLASS! ive found typically i like to shoot either off to the left or right AND above or below my pic, ie working with 2 different angles both left and right, and up and down, will give me the clearest pic. it just minimize the ability to get a reflection off the glass. never take a pic square to the front glass, it never works well!
and the rest basically comes down to patience and playing with the different configs of your camera, i like closeup, high iso, sometimes if i have a fish that just wont sit still i toggle the camera over to the moving target function (blur reduction). i notice typically i lose detail in color when i do that, but sometimes there is just no other way to take a pic of some species that refuse to sit still for the camera.
thats how i have my setup, off center, angled up/down and left/right depending on where the subject of the photo is. extra lighting, like if im angled up, i put the light below the lense, if im angled down, its above it, if its angled to the left, i put the light on the right, and vice versa, what your trying to do is keep from picking up a reflection from your extra lighting.
and take LOTS of pics. digital cameras dont require film, so dont been stingy with the shutter. its going to take some patience.
also, digital cameras with autofocus are a general nightmare for filming fish in a glass box filled with water. the camera usually tries to focus on the glass (if your square to it) or the substrate or decorations. basically the stationary stuff is what it tries to focuse on unless your fish is big and takes up most of the viewport.
so what i have found, alot of time you can trick the camera, you can focus it on one of the objects in your tank by tapping the shutter button to trigger autofocus, get a clear focus, then move the camera to your target (while still holding the shutter button to keep that focus locked in) and move it in and out till you get the same clarity on your target, and take the pic. (that technique is mandatory for me when i use my old nikon)
you just gotta play with it and see what you can make work for you in your situation with the equipment you have available. trial and error helps alot but without some atleast basics on how to film a fish in a glass box your going to have a long day on your hands and knees infront of a fish tank swearing wishing that digital point and shoot had a manual focus on it like an SLR camera lol.