The Linux and Windows binaries are built using gitian. Gitian is a system that builds the source inside an virtual machine running Ubuntu. By carefully controlling the build environment like this, it guarantees that everyone ends up with byte-per-byte the same binary as output. These are signed using GPG, and compared among developers before release. This allows everyone to verify that the distributed binaries are indeed created from the specified source code.
The script for the Windows build can be found here
. Note that it's built in a Unix environment, and is probably very different from how you'd do it on Windows itself. Still, it may contain some hints.