it's in the .js file:
fadeColor = "#FF9900"; // color to fade to
or do you mean the original link color? That's in your .style file
(Admin CP > Styles > Modify > Fonts/Colors/Etc)
Also, for all other users. As I'm not the original author if this javascript, I'm not able to support it. It's current state will
NOT support fading in <b></b>, <i></i> and other tags. I'm sorry

If you want to play around with the .js and get that feature working, please let us know in this thread!
- djr