For me these are the ones I'm using
Explosions_and_gunfire-The sounds are more loud and realistic
GWX - Late War Sensors Snorkel Antennas-You need it if you want to use the advanced GWX Radars
GWX - No Medals on Crew-More realism in my opinion
GWX - Reduced Positive Buoyancy-I like my boat stable in PD
GWX - XXI Hydrophone Fix
Longer Torpedo Wakes v1.02-The wakes give a touch of realism to the game
QueenMary JSGME-Great Ship, huge tonnage
Sobers_3D_Waves-Better looking Waves
Torpedo damage Final-Brilliant visual effects
Torpedo Eagles-The more emblems the better
TarJaks_Custom-Emblems-Same as before
In SH3Cmdr I use
Aircraft Markings Mod-More and better markings for planes
GWX Skin Pack - Capital Ships-It's the GWX Skin Pack Do I need to say more?
GWX Skin Pack - Destroyers
GWX Skin Pack - Escorts
GWX Skin Pack - Merchants
Intro Scenes-More Random Intro Screens every time you start the game
Up to Date Recognition Manual-A touch of realism and eye-candy in the game
VIIC41 Mod-A FANTASTIC Model of a Great Sub
Variable Renown for GWX-Year Based Renown (increases by 2% per year) for ships and planes
On top of that I use the brilliant skins from Danlisa, Fubar and Venatore for my sub (depends on the type)