I have come to the conclusion that it's not as simple as you'd think.
Basically I want my Dock to be completely transparent. So I set it to 2D and replace the left, right and bottom images with transparent versions of themselves. This provides the following...
What's this? The borders are gone, but what? Apple has made it so the background is a solid black color with transparency! Surely there must be an image to edit and make that transparent, right?
Wrong. Not in the Dock Resources folder at least. I have checked every single image. None provides that background.
"But, Jasoco" you say, "isn't there a file on teh internets that lets you make the Dock completely transparent?"
Well, yes. There is. It's called "Clear Dock", not to be confused with Unsanity's "Clear Dock", this is a folder full of resources to replace your Dock's originals with. But it is a paradox. This file makes the "1" images for the Dock border into 300x300 pixel images. Which while they do push the blackness down off screen they also create a sort of "dead zone". A portion on screen where you cannot click at all. This zone is made up of an area half the size of the 300 pixel image. Let me show you an illustration...

In this image you will note a colored area. This is for illustration purposes. Anywhere that color is, the mouse will not click through. So when the images are transparent, it's like having a piece of glass over the desktop. You won't be able to interact with the desktop no matter what. There is ANOTHER app on the internets called "Mirage", which after testing it out, turns out to be exactly the same thing. Same dead zone and everything. It's just the same hack in a pretty package.
"But, Jasoco!" you cry, "What about the 3D Dock? Can't you make it transparent and do it?"
Yes... but no. See, if you make the "curve" images clear, you end up with an ugly mirror... let me show you what I mean...

Notice the reflection of the desktop image clear as crystal and how noticable the blur is now. Plus the horrible angled ends. Looks fine when the image is filled, but when it's clear, it's not clear. See, the "opacity" of the PNG files creating the mirrored Dock simply tell the Dock how reflective to be. If I change the images to solid black, it is completely matte with no reflection. Hence being clear makes it completely reflective. (Side note, does it bug anyone else that the icons are overlapping their reflections by 2 pixels? WTF, Apple?)
I'm wondering if it's a PLIST preference. Like the color and opacity can be changed by editing a preferences file. All I know is it's not in the com.apple.dock.plist file. So, where is it? What controls that color and opacity?
Unfortunately, an app I used back in the Tiger days does not work on Leopard. "Transparent Dock" apparently set the colors via AppleScript. I assume Apple completely changed how the Dock is displayed.
A gold dubloon* to whoever can figure out how to successfully and non-buggy-ly get the Dock to be completely transparent.
*Or a hug and a thank you from the community.