On the SHIII Mods workshop forum you can find sticky threads that will give you some of the main overhaul mods that totally revamp the entire game experience. I played GWX3 for a long time until I got tired of hearing all the unnecessary and historically incorrect radio chatter from the enigma.
Basically you have to ask yourself what you want, and then start asking/looking around to figure out which ones fit your flavor so to speak. On a clean install of SH3, ensure Vanilla SH3 is running correctly without crashes. If you crash after installing a mod, it will be too difficult to diagnose if you don't do this!
Get JSGME, and put it in your ubisoft/SilentHunter3 folder (Or wherever your SH3 main game folder is). It will create a "MODS" folder, and then you just zip mod files to the directory for MODS. Go into your JSGME panel, and activate or deactivate as needed. Make sure to always read instructions cover to cover as you go along with the process (that's what they were written for). Some MODS come with multiple files that you need to activate in order in JSGME, hence why reading the installation directions every time is a must.
Whatever you do, don't come on the forums complaining that nothing works when you didn't read the instructions first. All too often people do that, and it's especially annoying for the people who spend the time writing the material for you.
Try it out, if you have any questions you know where to come for help. Cheers and happy hunting!
