@zedprime: FWIW, in Peacewalker: The Boss' horse is critically injured and Snake euthanizes it.
D-Horse is, as sure as you can be about anything in Metal Gear, a different horse :)
I'm still trying to really decide what I feel is going on here - but it seems clear that there's a strong Moby Dick metaphor going on here. There's a lot of symbolism to be drawn between Ishmael/Ahab of the book, and Ishmael/Ahab of the game (so far, at least).
And then there's the Whale.