I don't know if it's still revelant, but according to the first post (and post #432), you're looking for "Xen's Fallen Empire." I didn't see it mentioned again in this thread after that, so I'm guessing it hasn't been found yet.
http://www.oldschoolapps.com/blog/shameless-plug-for-an-snes-type-game
That's apparently a blog post that is fairly recent (from July 15) which contains a download link:
http://www.oldschoolapps.com/files/Xenv1.3.zip
It appears to be working since I downloaded it successfully. Whether it's the correct game or not, I am unable to tell.
Using the game's name as a search query for Google yielded results for only three websites, one of which was that blog (and another one being GamingW), so I found this one easily.
I just wanted to point out that I am the creator of this game, Xen's Fallen Empire. The website that was hosting the game for about a year got hacked, and I eventually gave up trying to save it, so I took the game down. During the downtime, I did an overhaul of the graphics, added a few bonus features, and then let it sit for awhile. As per the link above, you can find details on the game and try it out. Many bugs have been fixed, and some of the battles have been scaled to a more proper difficulty for their time in the game.
My brother (owner of OldSchoolApps) received an email regarding this thread. I can't believe people are searching for my game. Makes me feel kinda warm and fuzzy! I had been working on another game using RPG Maker XP, but never got that far. I may be starting up on it again. We'll see.
Thanks for the support to those looking for my game!