Heh. You are speaking to the world's bigest Eternal Darkness addict.
The game has three storylines based upon whether you picked the green, red, or blue artifact at the beginning of the game. The level design and layout is identical in any case, but there will be subtle differences in how you play the game. Don't be expecting big changes, just a new spin.
At the end of each scenario is a different ending, and when you finish the game with each, you unlock some bonuses. When you finish the game the third time, you get a special ending, with more content. what the content is, I do not know, as I have yet to get the third ending. To be fair though, I have been seperated from my copy for an extended period of time, and haven't had a chance. I have just rented the game though, and I am playing the third scenario when I should be studying for my exams.
EDIT: Bloodworth, ironically I did save green for last, and it's having the biggest toll on me. It's actually harder for me than red was, simply because I like to keep my green meter half full most of the time, and that's dangerous with the green scenario.