I understand Goldeneye (although a new Goldeneye eventually did come out, did EA repurchase rights to that or what?, would love to read that article too), but what was the deal with System Shock 2? Isn't it just another old PC game? Didnt know there was some licensing issues behind that game.
As for getting stuff to work, my best advice would be to run vmware. It isnt too hard to figure out how to set up and there are tons of guides online. Just set up a virtual PC with whatever specs you want and install DOS and Win98SE on it (or whatever the game you wanna play requires) and you should be golden. Good luck!