I assume from your posting here you intend to mostly run a U-Boat campaign. If you plan to play both sides of the war you need
Multi-SH4, which lets you have several game installations all separate from each other.
For the U-Boat side there is really only one must-have mod, the supermod Operation Monsun. It lets you have a campaign that lasts the whole war and run any of the major u-boat types.
http://www.subsim.com/radioroom/down...o=file&id=1097
http://www.subsim.com/radioroom/down...o=file&id=1403
Everything after that is icing on the cake.