I teach Perl courses pretty regularly as part of the computer science program at Marlboro College. We don't have an engineering program, though; it's a liberal arts school and my students tend to do cross disciplinary work that combines computers with music, dance, biology, or whatever.

Java and C++ are what I've seen as the most popular languages in college programs, though there's a fair amount of variation.

While I use Perl a lot and think it's a great tool, I also think its a mistake to rate a school as "good" or "bad" depending on whether or not they use your language of choice. IMHO, different languages have different strengths and weaknesses, and so a good computer science education should expose you to some of that landscape rather than leaving you feeling that your way is the only way.