The most secure (and proper) way is to have your Windows installed inside a virtualbox, and to route virtual bridge interface. Look "Whonix" for details, they use Debian for the guest OS, but Windows is also supported.
Other way (witch doesn't require virtualization) is to set up a new TUN/TAP interface with this tool:
http://code.google.com/p/badvpn/wiki/tun2socks
and then mark it as a default gateway via
route add
