Virginia, Maryland, Temple and Pitt all won games they wouldn't have won if PSU had been at full strength. I don't know that it would have made much of a difference in any particular program. The rise and fall of programs is over a large number of years.
You could argue that the relative decline of Penn State in Paterno's last 20 years allowed the rise of Rutgers under Schiano because Rutgers was able to beat out PSU for quite a few NJ and Pa. recruits. A lot of talented Pa. players spurned Paterno to play for Maryland, VA and Va Tech or went further south to Fla.
But I don't see any lasting effects. Just about everything Schiano built in credibility for the Rutgers program is gone. Maryland is doing well now, but going forward Penn State is going to generally beat Maryland for Delmarva and Balt-Wash metro area players.
U.Va. is down, Va. Tech is in transition and UNC is not a power. So it's been a good time for Franklin to re-establish ties in Va. and the Carolinas which used to be almost like home territory for PSU.