Considering that it's X11 you're talking about, I don't think you should look at what applications do, as the behaviour of what happens often differs within the application: different widgets do different things. Take a simple Perl-Tk program using all the default bindings. Middle clicking after a selection will have different effects depending on whether you click on a button, a label or an entry widget.

I've never used Padre (and I doubt I ever will), but AFAIK, Padre is a graphical application, and hence I'd expect different things to happen depending on where I middle-click.