Well, it's not easy. I threw away hundreds of bad photos to find a few gems. In the super dark areas, you'll have to shoot at high ISOs if you want a chance to shoot with a decent shutter speed, and that's with an image stabilized lens.
To reduce glare and reflection, you have to be able to get close to the glass and/or stand at an angle to avoid reflection. If you have a polarizer, I suggest using it in areas that aren't dark so you can see clearly through the water and cut down on reflections. In dark areas however it won't work so well since it can drop your exposure values down a couple of stops.
Finding fish or animals that don't move much is also key!
Sounds funny, but it's true. Trying to take a picture of a moving fish behind glass in the dark with a 1/6th shutter speed is very difficult.
One major mistake I made is when I exited the dark aquarium section to go see the seals, sea lions and all that stuff outside, is that I cranked my ISO down too low. I was so happy to be shooting at 1600 anymore, than I over compensated and shot at ISO 100. My girlfriend kept her ISO at 640 and above even though we were outside, and that allowed her to shoot at like 1/1000 and faster for some shots. I compared my work with hers and hers were so much sharper and had a much higher win/loss ratio for good and bad pics.
Next time I'll keep it in mind though, keep your shutter speeds high if you are shooting wildlife and it's active. If it's stationary, then going for max quality is fair game of course.
If you find yourself in a dark situation though and you are trying to take a crisp picture of a moving subject, the only advice I can give you is to crank up the ISO, set your shutter speed as fast as you can without under-exposing, use manual focus so it doesn't hunt on you, tuck your elbows in close to your body, breathe out slowly while shooting in continuous mode and pan with your subject to keep them in frame.
Superb photos! The first and third photos are my favourites, very well done! :]
Seeming as you've done aquarium photography, can you offer hints on shooting fish through glass in a tank in these big aquarium places? Particuarlarly those tunnel areas where the shark attractions are usually located? I got poor results when I tried to take photos in dark through Aquarium glass.