Ok, now for the mosty part I am just repeating here what swanson said in this forum post but this is how I ended up getting Sim City 3000 to work. I would also like to say that I will probably use this archive for other loki games that I had problems with and how I got them to work. I currently own Sim City 3000, Sid Meisers Alpha: Centauri, Heroes of Might and Magic 3 and Myth 2. (I also purchased Heavy Metal 2 off of ebay, but that has not arrived as of yet)
I have had little luck with Myth 2 so far, but I haven't made enough progress to mention that here... yet.
Anyway, so back to business. I can install (as root) Sim City 3000 just fine.
/mnt/cdrom $:sh setup.sh
But when I went to run the game I would get an error that a library was missing. I had tried to install (since I'm in Gentoo I used portage) several different libraries that different places online had hinted might help. (Basically ggi, gii, the loki libraries and the old voodoo drivers) Nothing helped. I finally came accross the forum post which talked about this problem. Seems the solution was to rebuild some old libraries (which were named Loki_Compat) and to specify those libraries when running the binary by doing the following:
$LD_LIBRARY_PATH=/path/Loki_Compat/ /path/Loki_Compat/ld-linux.so.2 /path/SimCity3000/sc3u.dynamic
The trick worked perfectly, although I noticed that the game runs a little sluggishly on my machine with a high resolution, I am very happy that is simply works, since it is farther than I have ever gotten with this game. Thanks swanson :)