This is what I have at the moment.
[TMO] Tigger Maru Overhauled - Fixes many default in-game stuff, beefs up A.I., improves many things (graphics, gameplay etc.)
[RSRDC] Run Silent, Run Deep Campaign - Mainly historical stuff like historical shipping routes.
[OTC] Optical Targeting Correction - Mainly deals with visuals and scopes I think.
Traveller's Mod - Sort of like TMO, fixes a lot of things plus makes the game more challenging (e.g. start with no renown, your sub will easily take more damage than default)
If you're just getting into mods I highly recommend starting out with just TMO for now.