I don't know how much about what retaking courses/taking graduate courses would do, but it certainly wouldn't hurt. Showing an effort to stay engaged in the field and make positive progress would always look good. A GIS certification would be really helpful, as would taking a course in R programming language. Internships would help a lot if you will be able to do some alongside your work.
From what I've been taught and told by potential PIs, experience goes a long way. Possibly one of the most important things you could do to improve your application, at least from my understanding. If you are limited in time, out of everything here I would prioritize at least one hands on internship that aligns well with what you want to study in grad school and what you want to do for an end goal career, after you finish your education.
GIS and R are becoming increasingly important tools in this field. My undergrad required we learn GIS because its become so prevalent and I think R will be going the same way in the coming years. Professional conderences I have attended have stressed the importance of R as the best tool for biological dtata analysis. In my case I didn't get to take a course in R, but I know my top choice program offers a workshop so I will definitely be able to catch up. In 3 years, learning R might have become more standard amongst fresh graduates, so it may be worth learning to be competetive.
I am finishing up undergad and applying for grad school for the first time (straight to PhD, coming from a Wildlife and Fisheries B.S., going into Ecology and Evolution) so take this all with a grain of salt. My experience is limited. But this is what was stressed as important by mentors and advisors at my school and some by the graduate PI I've been corresponding most with.
