I have a solution that may help.
By using Xming you can run these Linux Applications Locally.
coupled with the slim XFCE-Panel (XFCE is a desktop environment similar to KDE or Gnome) you can run all your Linux applications on your windows PC.
All the important setup info can be found in this Amahi XFCE panel site
The applications are installed on your HDA, Xming works as a Xserver Just like any regular desktop session or VNC session.
I have chosen to use multiple windows (One window for each application) as it provides the most seamless expereance.