Well my preference is GWX since I've tested it, but in general, it's best to find a supermod which has already got many of the smaller ones already in it.
SH3 Commander is a program which most people use and I highly suggest. A new version will be out soon which is incorporated to work well with GWX.
For now, I'd suggest just playing the Vanilla version and then when you get that supermod, you'll see how big a difference it really makes.
There are a few others I've used in the past like SH3gen which gives you locations of enemy ships during certain time frames and intelligence on where to go and what to look out for like subnets and mine locations at enemy ports.
The weather mod was good when I used GW1.1a. I don't know yet whether it will be needed or even work with GWX.
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