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-gameThat's apparently a blog post that is fairly recent (from July 15) which contains a download link:
http://www.oldschoolapps.com/files/Xenv1.3.zipIt 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'm also curious about what purpose (and how) you have to have all these games saved(?), other than posting them in topics like these.
You can find the completed version of The Legend of the Philosopher's Stone here:
http://www.rpgrevolution.com/game-downloads/the-legend-of-the-philosophers-stone_144.html
I downloaded it, but the folder inside the .zip says it was last modified on 16/06/2005. I have a .rar of LotPS I downloaded in May 2009 with a folder in it that was last modified on 19/05/2008, so I'm doubting the former is the full version. The "last modified on" date could easily be changed, so I looked at the amount of maps and the 2005 one has 63 less maps/areas (214 vs 277). The 2008 one I have is apparently the same one that post #600 Jabbi has, ending after a certain prison.
Edit with request: For nostalgia, I'm requesting what was probably the first RM game I played. However, I do not remember its name. I remember a few things about it though.
Pretty sure:
-Main character was named "Mage";
-"Mage" used the RTP faceset with a male with blue hair covering an eye;
-"Mage" used RTP charset corresponding to that faceset;
-Had a short demo (and maybe the only version of this game?) ending after a Golem(or something else big) boss triggering as the player enters a town is defeated;
-An old man NPC that was somewhat important named Tellah;
-"Tellah" used the charset of the RTP old man in green(?);
Remember vaguely:
-A party member that used the default bow/arrow animation;
-A dungeon that had arrows that might or might not have sent the player in the direction pointed at;
-About 7~8 years old (I suppose this can be considered a guess?);
Guessing:
-Probably only used the RTP graphics
As "Mage" and "Tellah" are very common words (with the latter being even somewhat related to the former), I don't think I'll be able to find it by using those as search queries. I wasn't the one who downloaded it so I don't know what kind of website it came from, but it probably wasn't very popular, making it even less likely I'll ever find a page that still exists with those two terms (and RM2K) and the game together.