Myself, I have tweeked almost every sound file in the game (except speech; I like speech the way it is). Most other sounds have been personally customized to my liking.
The same goes for most of my graphic files. At some point or another, I have modified almost every TGA in my database... Ok, not every TGA, but all of the important ones. Airplanes, subs, ships, sky, water, terrain, special effects... You name it, I messed with it...
Also, I have so so many gameplay tweeks, that I have no idea what version I run anymore. Call it a hybrid 1.4b, IUB, RUb, HT, IC, Atm8km...
And in order to accomadate this, I don't use JSGME (gasp!). It would be too difficult if I didn't manually do everything myself...
I guess you could say that my version of SH3 has been
Marhk'd off. 