Sorry for the double post but check these out for a lot of help for Mods selection!
Mod loadout/order to help find some popular Mods:
http://www.subsim.com/radioroom/forumdisplay.php?f=249
Generic Mod Enabler:
http://www.subsim.com/radioroom/showthread.php?t=169092
Must have Mods (in my opinion):
Great User Interface. One of the (two) most popular UI Mods for Sh5:
http://www.subsim.com/radioroom/showthread.php?t=166093
Another good interface, though I don't use it it's also popular:
http://www.subsim.com/radioroom/showthread.php?t=173147
Churchs Keyboard Commands; adds the majority of the missing commands to the game:
http://www.subsim.com/radioroom/showthread.php?t=163444
Capthelms Audio Mod; Awesome sound Mod:
http://www.subsim.com/radioroom/showthread.php?t=163530
Automated Scripts to help you do some tasks:
http://www.subsim.com/radioroom/showthread.php?t=173805
Mighty Fine Crew Mod; helps improve your crew (morale) and adds some animation:
http://www.subsim.com/radioroom/showthread.php?t=163591
Uboat Historical Specs (UHS); good Mod that fixes some bugs with the U-boat and makes the submarine more realistic:
http://www.subsim.com/radioroom/showthread.php?t=168012
Adds the historical Flags (Swastika included.. dont download if you dont want it):
http://www.subsim.com/radioroom/showthread.php?t=162671
SteelVikings Interior Mod; wonderfull interior Mod to spice up your submarine:
http://www.subsim.com/radioroom/showthread.php?t=171415
More Crew Commands Dialogue:
http://www.subsim.com/radioroom/showthread.php?t=166236
Environment Mod 3.2; good Environment Mod (may make your game CTD):
http://www.subsim.com/radioroom/showthread.php?t=166178
SteelVikings ShadowImprovement (will help your framerate):
http://www.subsim.com/radioroom/showthread.php?t=171982
SteelVikings Underwater Mod:
http://www.subsim.com/radioroom/showthread.php?t=173150
BARF 1.3; nice fix to the Health of the ships and their behaviour:
http://www.subsim.com/radioroom/showthread.php?t=164953
IRAI (V. 0.20 currently) is good for AI tweaks, but if your just starting out I'd stay away from it:
http://www.subsim.com/radioroom/showthread.php?t=171973
Feared Hunters 2.0 another good Ai Mod, not as hard as IRAI:
http://www.subsim.com/radioroom/showthread.php?t=167682
Uboat Killer Ai Mod, Not as hard as IRAI or Feared Hunters:
http://www.subsim.com/radioroom/showthread.php?t=165886