This 5 mods must have imo:
-Manual TDC only
TDW multiple UIs
http://www.subsim.com/radioroom/showthread.php?t=166093
-Ship Damage model adressed
-Damage effects like listing etc
TDW FX Update
http://www.subsim.com/radioroom/showthread.php?t=174511
-more dynamic campaign
OHII ofc
http://www.subsim.com/radioroom/showthread.php?t=189818 (but I don't use it still because of my old PC)
Dynamic Enviroment
http://www.subsim.com/radioroom/showthread.php?t=182377
TDW IRAI
http://www.subsim.com/radioroom/showthread.php?t=171973
About crew skills - I just don't learn them
Other mods depends on your tastes and you should discover them yourself. Start from sticky threads above and this topic:
http://www.subsim.com/radioroom/showthread.php?t=173193 