Does PIE support color-stops with percentages, so for example, you can have the top 10% of the gradient going from red to green and the bottom 90% going from green to blue?

Here's how it's done in webkit:
background: -webkit-gradient(linear, left top, left bottom, from(#ff0000), color-stop(10%,#00ff00), to(#0000ff));

You can, of course, easily simulate this when the gradient is strictly vertical or horizontal, but not when it's angled...

PIE supports the CSS3 spec syntax, so yes multiple stops with percentage offsets are supported. You can also use length units other than percentages in the stop offsets, which isn't supported by Webkit's syntax.