This glow notification effect happens when the tab's title is changed.
To see, create an HTML file with some Javascript that changes its title after a moment, like:
setTimeout(function() {
window.document.title = "New title!";
}, 3000);
Open it, pin it, then change to a different tab. After the 3 seconds, the pinned tab should glow.
Firefox 4 also does this.
Oh, actually read what you were trying to do now. Don't think you can change the colour, no.
