You can mount the SD card as a folder within the Program Files folder on the C drive. This allows for installing programs onto the SD that would normally be restricted to C:\Program Files, as long as the installer allows you to select the folder.
This is done through the Control Panel, Administrative Tools, Disk Management. Select the drive letter for the SD card from the list, right-click on it and select "Change Drive Letter and Paths". Click "Add" and create a path to the SD inside the existing Program Files folder.
I did this and created a separate Program Files folder on the SD for installing programs, and it works well. Have this on both my Mini 9 and Eee.