Most of them are described in the 2.0 manual, but here's a quick rundown:
3rd Flotilla - Changes the
10th flotilla to
3rd flotilla. So instead of two Lorient flotillas, you can base out of La Rochelle now too.
1500m bearing overlay - A very nice overlay when zoomed into the map around your ship.
Alternate Dial Faces - Much cleaner dial faces in game and on the interface.
Enhanced Nav Map Plotting Tools - Umm.. no idea.. I think this is the same as the ? icon on the map actually.
Harbor Traffic Add-In - Additional ships and stuff in harbors to make it feel more alive.
Minefield JPGs - Pictures of the minefields of friendly ports from the mission editior, they end up in your main install folder.
NYGM Minefield Mod - Makes mines invisible so you can't see them with external camera or periscopes.
Restore Gods Eye View - Removes the 'fog of war' features and lets you see the GPS satallite features of the map during combat
SH3 Commander Optional Updates - Depth keeping mod and malfunctions run by SH3 Commander.
Single Merchant Contact mod - You get radio reports of single contacts instead of just convoys.
The mods in bold I personally consider must haves.