Here are the steps to get Wing Commander III and IV running (for me).
1. Right-click the WC3.EXE (on the first CD) and select "Run with VDMS".
2. Select the second Option "Set up a custom configuration"
3. ..."Create a new configuration from scratch".
4. ...(Advanced)
5. Under the "Compatibility" tab you deselect "Enable expanded memory (EMS)" and select "Enable low-level CD-ROM support (MSCDEX)".
6. Under the "Joystick" tab you click on "Inputs mapping..." and choose one of the joy*.map files. (You can take a look at the joy*.map files with your text editor and even simply make your own one)
7. Close the VDM Sound configuration with a click on "OK".
8. Deselect "Remember my settings", select "Add a shortcut to my desktop" and finish it.
9. You will now be presented with the Install-Screen of the Game.
Even though it's pretty straight forward I will tell you the right sound settings.
Card = Soundblaster/Compatibles
I/O = 220
IRQ = 7
DMA = 1
10. After the installation you can copy the "Alternate Joystick Routines" you can download for
WC3 and
WC4 into C:\WC3 (or your WC4 folder) and double-click it.
11. All you need to do to run the Game now is to double-click the shortcut on your desktop.
Please try this and tell me if you still got problems.