There are so many mods that do so many things... generally the best advice is to spend at least a little time with the stock game, to see what things you would most like to add or enhance (or get rid of entirely).
If you have a 64 bit OS and 4GB or more of system RAM on your 'puter, consider using the 4GB patch for the game's .exe file as this will allow it to access up to 4 gigs of RAM (if available) as opposed to the 2 gig max it will use with an unpatched .exe file. This may be crucial if you eventually want to use some of the bigger, more resource-hungry mods out there.
You can check out the sticky threads for the various supermods (GWX, WAC, NYGM, Living Silent Hunter) in the Mods Workshop forum for more info on what they offer. A lot of smaller mods are designed to be compatible with one or more of the supermods so if you really plan to mod the heck out of your game, choosing a supermod as a base on which to build is probably a good idea.
MultiSH3 is a handy little add-on that will allow you to run more than one installation of the game on the same computer, so that you can keep a stock installation plus have separate installations for one or more supermods as well.
JSGME (JoneSoft Generic Mod Enabler) is a must-have as the best way to enable/disable mods with a minimum of hassle.
SH3 Commander is a stand-alone add-on that will give you a whole bunch of cool options that you won't find anywhere else.
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