Look around the room where you will be using it and measure things in the room. In my case, I was building a stand for a 29 with a space under it for a 20H. When I looked around near where I would be putting it, I found my TV and entertainment center nearby. When I thought about it, the tank is about as tall and wide as my TV so I set the stand height to put the tank about the same height. This way the room would look more balanced rather than have a bunch of odd heights on things in the same room. It turned out the room to service the 20H would have been a little cramped so I compromised and moved it up about 2 inches to set the top of the hood about even with the top of the entertainment center.
Conclusion, look around where it will be and take your cues from the location rather than forcing the room to accomodate a particular design. It is one of the benefits of building a custom stand rather than buying the one at the LFS.