In a nutshell, JSGME is a mod management tool that simplifies, well, managing mods.
With this tool, just drop your mods into a folder called "Mods" and then you can easily pick and choose which to use via a nice gui. SH3 Commander is a launcher utility that has numerous tweaks for crew management, flotilla data, time between patrols, etc. Very easy to use. And you can export patrol and crew reports out to .html files.
GWX - where do I start? A labor of love by the mod community. HUGE mod. Changes numerous aspects of the game for the better. You'll read much more about it on these pages.