The game Pray has a history almost as good as Duke Nukem Forever. What started in 1995 and was released 2006 has seen many different versions. In 95 the story was you are abducted from Earth, and wake up with a biotech suit on and the suit is apart of you (something like the Borg from Star Trek: TNG). By 2006 it was on the Doom 3 engine and you a Cherokee named Domasi Tawodi (aka Tommy) trying to save his girlfriend Jen after being abducted from a bar in Oklahoma. Over at apogeegames.com there is a full history of this game with quotes from the many people that worked on it over the years.
From the beginning, Prey was designed multiplayer, user modification, and scalability in mind. Prey even included a C like scripting language, much like Quake and Unreal have. The 3D engine started off as software only, but later added hardware support for 3D cards. Also dynamic lighting was a big feature of the early engine. The online portion included a feature where the player is able to seamlessly jump from one server to another. This might not sound like much today, but in early 1996 this was huge.
If you have played the game or you are thinking about getting it on Steam you will want to read this.