Right click on sh3.exe and click the version tab. It must be:
Version 1.4.0.1
There are many supermods.
Mod = short for modification.
GWX 3.0
NYGM
LSH3 4.0
WAC 4.0
The above are supermods.
Install SH3 (clean install), if need patched you download the patch an ubi.com.
Download
http://www.users.on.net/~jscones/software/products-jsgme.html this great program and put the jsgme_setup.exe in:
C:\Program Files\Ubisoft\SilentHunterIII
Double click the jsgme_setup.exe in the above folder.
Make a folder called MODS.
Download 7-zip at:
http://7zip-new.com/
Download a supermod (stated above, see the four I gave you) and extract a 7z file to C:\Program Files\Ubisoft\SilentHunterIII\MODS
If you want to install GWX, they have made a simple exe file now, just run the exe.
If you want to use SH3 Commander, download this great program too and install GWX3_CFG_for_SH3Commanders.exe.
Every supermod (only WAC don't have it) have special files for SH3 Commander.
With SH3 Commander you can adjust almost everything concerning game play and other things.
I hope this helps!