I don't think there are any general skills that all "academic programmers" have because this is a profession where you can be a good programmer but have a very different skill set from other good programmers.
Any programming job will require you to have good problem solving skills and the ability to pick up new languages/technologies. Beyond that, there are two broad "fields" where programmers can go into: tech companies and non-tech companies.
Most non-tech companies hire IT people to either maintain their current systems or work on projects for the company. In these environments, the programmer is not the focus of the company but instead is more of a support role. They'll want you to have knowledge of whatever technologies they use, and to have the flexibility to work on different projects depending on what's going on.
On the other hand, programmers are the bread and butter of most tech companies. They're looking for people who know their technology stack or are willing to learn, and for people who are good programmers. Oftentimes, tech company interviews involve brain teaser or programming challenges that involve concepts like recursion, dynamic programming, etc. It's generally understood that you have to be an above average coder to work at a good tech company.
So in the end, there are no specific "skills" per se. Someone who's been coding in Java for 10 years and nothing else will certainly be lacking in Ruby on Rails "skills," but that doesn't make him or her a deficient programmer. To get a good job, you need to make sure you're a competent coder, a good problem solver, and someone who can learn new things at a quick pace.