Being a longtime Xcode user, I’m used to putting things like:
#pragma mark Interesting Stuff Here
between functions/methods, which makes it much easier to find groups of similar functionality within a file. The bookmark Interesting Stuff Here will then appear at that location relative to other things in the function popup.
ScriptDebugger offers Markers, but they appear at the top of the function popup, making it less helpful. Could you change it (or add a pref) so that it behaves like Xcode, putting the Markers inline where they should appear?