When it comes to making anything for the aquarium, do NOT use polycarbonate (i.e. Lexan). It may look and react similarly to acrylic, but it is NOT acrylic. Polycarb will eventually break down, yellow and become brittle when exposed to UV rays (unless you get UV coated polycarb), whereas acrylic won't. It was mentioned that PC might be useful for sumps or other things that don't need to be asthetically pleasing. But if you ask me, I wouldn't use it at all. Most of your stuff will be exposed to light somewhere, and nearly all light sources will give off SOME UV rays. Unless you put this thing in the dark, I wouldn't trust PC with anything. If you're gonna do it, do it right the first time. Acrylic all the way! Just my opinion...
And if you need acrylic, I've found that the local plastics shop tends to sell scrap pieces at VERY reasonable prices. I got a piece the same size as HD was selling at 1/3 the price and it was thicker, too. They're not small pieces, either. I'd check plastics shops first. They'll also have the Weld-On solvent adhesive you'd want, as well. Most other places won't sell that, as it's industrial adhesive.