Welcome Aboard!
First, about Commander. It's not really a mod, but a tool that controls and adds to certain aspects of the game from outside the game itself. You won't be sorry you installed it.
Supermods:
GWX
LSH3
NYGM
WAC
I've given the links to the start of each supermod. There are hundreds of pages, and I don't expect you to read all of them. I just wanted to give an idea of what's there. Each one of them takes a different view of which direction the game should go, and each one provides a different experience.
http://www.subsim.com/radioroom/show...17&postcount=4
I did another comparison, but I can't find that post right now. In any case, please ask all the questions you want. There are fans of each supermod who will gladly tell you what they like about it and what they've added to make their own experience better.