Simply put, there is a lot of stuff. Very few mods have any intrinsic problems. Mod conflicts are frequent, but seldom fatal and always visible with JSGME. And most mods have documentation ranging from acceptable to excellent that will alert you to potential conflicts. The subject is vast and fuels two forums on this site just about fulltime, which is probably why you didn't get an immediate response.
I can post my mod list, but it's very idiosyncratic. Works for me, may not work for you. It also involves some tweaking, which is hidden behind the curtain, to allow some mods to work together. The last mod, my homebrew called BW On-Top, contains tweaks, merged files, and assorted fiddles which make everything play nice together. Withoout it, you could experience funnies. Caveat ludius.
Generic Mod Enabler - v2.6.0.157
[C:\SH3-WYGM\MODS]
NYGM Tonnage War V2.5 – Stand Alone Version
NYGM3_New
NYGM3_6D
NYGM Tonnage War Minefield Mod
NYGM HiRes Submarines
NYGM 3.6D zigzag campaign layer
Merchant_Fleet_Mod_3.2
Harbor Traffic Add-In
AllAirTorpedoes
Scirč-Tikigod- repeated order
BritishAsdicMkIFinal
EAX_Sound_Sim_SH3
DD_OH_V3.09_20091209162038
FM_NewInterior v2.1D
Carotio_SH3_ClothesHatsFacesSkilledCrew
NeuUZO&PeriV.2
Capt. Teach's SH3 Color Icons for GWX 3.0 (Standard)
TorpedoTubesFfireFinal vStock
Spirit of machines
Bearded faces
M.E.P v4.2
M.E.P v4.2 to v4.3
Optional - FSF for MEP v4.2
Optional - ShipVanishingHull for MEP v4.3
M.E.P v4.2 - VisualSensors for NYGM 3.6b
New _hydrophone _layers for SH3 v2.0_NYGM
Rbs1_SH4_Effects_GWX_21_204f
Thomsen Ship Param Mod (MFM)
DeckKannon
Red Night Map
Seenot-Leuchtrakete - Do it yourself
Hitman_GUI_NYGM3_1.1
Van1920x1080 v1.1
Supplement to V16B1 - NYGM
Stiebler4B_Addon_for_V16B1 - NYGM
O2-Gauges v2
BW On-Top Mod WYGM v1.0.71
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