- An open source GUI for sorting spikes. When you put an electrode into the brain, you often end up recording the "sounds" of multiple neurons firing. To make sense of what's going on, you have to identify which spikes came from which neurons. While there are fully automated algorithms for spike sorting, they aren't widely used because people don't trust them to work on real recorded data. Even if you use them, you probably want to check their results later, and you need a good GUI to do so. Right now, the "state of the art" is Plexon's Offline Sorter (http://www.plexon.com/products/offline-sorter%E2%84%A2), which is slow, occasionally crashes, and costs thousands of dollars per license. It's mostly a GUI, and replicating it would probably not require much domain-specific expertise. The fact that it's closed source actively prevents the development of better partially supervised spike sorting algorithms.
- Better fMRI data analysis tools. See https://news.ycombinator.com/item?id=5239530 for some previous discussion.
- An open source replacement for MATLAB that is familiar to users of that language and encourages modular design and has a JIT that can achieve C-level performance. I am betting that this is going to be Julia (http://julialang.org/), but there's still plenty of work to be done before Julia is ready for people without substantial programming experience.
- Better tools for visualizing high-dimensional data sets. I'm not actually very familiar with what's been done in this domain, but I feel it's something that isn't often attempted because there's little overlap between experienced graphics programmers and scientists. A good way to visualize your data can save you days spent performing statistics.