WELCOME ABOARD!
For US fleet boats start with either TMO (Trigger Maru Overhaul) or RFB (Real Fleet Boat). They take different approaches to the game, but both are great. There is a tool called MultiSH4 that lets you run several installations of the game, so you can try both without having to take one out and put the other one in. For either one there is a campaign called RSRDC (Run Silent, Run Deep Campaign) which makes the Pacific war much more historically accurate.
If you want to run a u-boat you'll need Operation Monsun, which creates a very nice Atlantic campaign. Again, MultiSH4 is your friend. Most of these are available here in the Subsim Downloads section.
As mentioned, JSGME is a too which allows you to install mods easily, and more importantly uninstall them again. Get it here:
http://www.subsim.com/radioroom/showthread.php?t=173324