The latest released version (xmakemol-5.16.tar.gz) is available from Savannah. Other versions may be available here.
Savannah also hosts the XMakemol CVS repository, which includes details of how to check out and browse the latest source.
XMakemol packages for the stable, testing and unstable branches of the Debian GNU/Linux distribution are available. The basic xmakemol package doesn't include OpenGL support, whereas the xmakemol-gl package does.