It all depends on what YOU want out of the sim. I myself have about 20+ mods installed and love it. Go to
http://u-boot.realsimulation.com/ and click on articles on the left side then on Silent Hunter 3 Readme files (354) and browse through some of the mods that look interesting to you. You can read about what they do and what they effect. Then when you find one "or more" that you want to try go to the download page and download it to a file on your desk top. (I made a file that is called Sh3 mods).
Now BEFORE YOU INSTALL ANYTHING, download and install the jsgme.zip file in the "must have section". THEN unzip any mods you have downloaded into the "mods" folder that will now be in your programs/ubisoft/silenthunter 3" folder. This will allow you to install any mods so you can try them and and if you do not like them you can EASILY uninstall them without having to reload a fresh SH3 install
.
Any questions ask here on the forums. I hope this helps and does not appear to be talking down to you if you already know more than this.