This fantastic game actually has four endings, not three. Let's see if I can remember how to get them..
Good Ending: Keep your corruption gauge as high as you can get it by rescuing humans and walking past them to collect the blue-white orbs they spit out at you. Don't kill or rape any humans, then beat the final boss with your soul corruption maxed and the light orb equipped. This is the 'normal' ending and I personally think it kind of sucks. It's your base for getting all of the other endings safely, however; if you want to see them all, go through the game like you want the good ending and keep a save at the final boss so you can switch it around.
Bad Ending: The same as above with a twist. Kill a lot of humans (I'm guessing 200+, but haven't experimented a whole lot with it) and then defeat the final boss with the light orb and high soul corruption like in the good end. You'll know you got it right because the boss will rage when he's defeated, saying that in your heart you want darkness and destruction. Once you fulfill the requirements for this ending, it's impossible to get the good ending. So get the good one first. Relm is raped in this ending, but it's actually pretty boring, so... Don't get your hopes up.
Neutral Ending: In previous talks with people about this game, we concluded that this one is probably the true ending. It's the same as the good ending, but you fight the final boss with the dark orb instead of light. You should start the fight with your soul gauge high and then be in brute status by the time the FIRST fight with the final boss ends. Then you defeat the second form with the dark orb as well, after which you get to fight the 'real' final boss, which is actually the boss from the evil ending. It's a plot-twist 'I'm the real bad guy' type of ending, and it's probably my favorite of the bunch.
Evil Ending: Be in brute status when you enter the final boss fight, defeat his first form with the dark orb. You'll then switch sides, meaning you don't have to fight his annoying second form (hooray), and go through a small extra area where you have to kill humans. Then you get to face a different boss instead. I don't believe the 'kill 200+ humans' requirement from the bad end applies for this ending, meaning it's just as easy to get as the good ending.
Also, if you finish the game quickly with a high item completion percentage, the background image for your 'thank you for playing' screen changes, Metroid-style. My quickest and most accurate so far is 3:48 with 98%, which shows Relm in a swimsuit.