Mostly Matlab, Python, and R, with a few things that have tight time/memory requirements in C++. Matlab was really popular in neuroscience for a very long time, so we still have a lot of code in m-files, but most labs are moving towards Python (and a few towards R).
The code quality varies a lot. Some of our "core" stuff is great, but there's also a lot of stuff that was written quickly and meant to be run once ("let's just try it"), which is cold comfort when you find it years later.
People also come in with varying levels of programming skill. I'm going to try to do actual code reviews with the undergrads this summer to see if we can't make our stuff a little less embarrassing.
I'll add, I work in a lab and have seen the stuff of nightmares myself.