Presuming you are running stock SH3 patched 1.4
SH3Commander can tweek several things such as game play settings and gun load times. There are some other tweeking exe's that modify other game files you can change flak gun load times etc. But these are not mods so to say, actually programs to alter game files before you start the game. I don't belive anyone here wouldn't recomend Commander's options btw.
For actuall game mods there are loads of individual mods and there are also supermods like NYGM, GWX & War Ace Campaign.
I have a preference for WAC, the new version Rocks
Most mods can be installed with another program called JSGME (mod enabler) except for GWX. The forum has sticky threads for mos of these mods. On the SHIII forum there is another sticky you can find links and information.
The UBIsoft forum also has similar sticky threads/links.
The UBRS site is - I dunno what's goin on over there.