Since I don't have a tank yet, I'm afraid I don't at the moment, but I can give some ideas of what I see the pitfalls being...
For consumer digicams, its actually a little easier because you don't have to deal with a paper-thin depth of field at wide aperatures. When I've done shooting through tank walls at aquariums and zoos, I'm always shooting fully open, F2.0 or F2.4 depending on how far zoomed I am.
A tripod is a must obviously. One other thing is the subject. If you're taking a picture of a coral or other relativly stationary invert (this wouldn't apply to soft corals that move a lot in the current), you'll get a better picture if you push the limits of the shutter speed to as low as you can. A longer exposure tends to be smoother, to a point at least, since digital cameras introduce noise after a certain amount of time.
Anything fish related though, I'd put it on a tripod, be in aperature priority, and shoot fully open. For inverts, just play with it a bit, but always shooting at the lowest ISO possible.
Another thing that can help a lot is a cable release if your camera supports it. A very slow shutter (1/4s or less) will often give a very smooth effect on a scene where there's some light/water motion but not much of the actual subject moving, it tends to defocus the background and give a silky kind of look, which keeping the stationary subject very clear. Unfortunatly, even with a tripod, pressing the shutter without a release is often too much and you're get noticable camera shake in the final image.
The best advice though is to just try things and see what you like and don't. =) A little fill flash combined with a long exposure can change the texture of an image significantly while still freezing motion, an extremely long shot with fish and stationary corals in the frame can wipe out the fish completely even if its in the way as long as its moving fast enough. And when push comes to shove, photoshop is your best friend. There's an amazing amount of detail you can pull out of a digital image if you learn how to apply masks and sharpening in the right areas.
-Dylan, the verbose
