Beyond Compare 4.1 and newer require matching package and OS architecture (amd64.deb or i386.deb). Beyond Compare 3 - 4.0.7 require the i386.deb package on all supported versions of Debian and Ubuntu (32-bit and 64-bit).
Beyond Compare 3 on Debian 8, 9 64-bit
Enable 32-bit architecture support: sudo dpkg --add-architecture i386
Graphical Install
Double click on the .deb package to install using the graphical package manager.
Terminal Install
wget http://www.scootersoftware.com/bcompare-4.3.7.25118_amd64.deb
sudo apt-get update
sudo apt-get install gdebi-core
sudo gdebi bcompare-4.3.7.25118_amd64.deb
Terminal Uninstall sudo apt-get remove bcompare