I second Abigail's suggestion. This also solves the problem of storing additional data files. Just use /opt/myapp/(data|sounds|grapics|...). Some applications like to install themselves as /usr/bin/myapp, then proceed to install files into /usr/share/myapp/. I prefer the first approach, as it keeps everything nicely bundled together. You can always add scripts to /usr/local/bin to put your app in the path.

But of course, with opinions varying greatly, it is best to give the user a choice. Some might even want to install your app in a homedir on a shared server. That's the beauty of configure --prefix=/path...