I would like to see a wide variety of software tools developed.
I have performed neuroscience analyses using expensive proprietary programs, or custom-designed software written by amateurs. For example, in my previous lab, we analyzed data using Vector NTI, which costs $1000/year, and has an awful user interface, wasting time. In my current lab, we analyze multielectrode data using software written by the Buszaki lab. This software works, but is slow, requiring a high-powered computer to run overnight to analyze one piece of data.
The NIH has already developed one nice piece of software, ImageJ, which is used extensively throughout neuroscience. The programs I would like to see (from my own experience) are an update of ImageJ, a DNA analysis tool (primer design, sequence alignment, etc.), spike identification, and spike clustering. Given the highly computationally intense nature of some of these programs, they should furthermore utilize the power present in modern graphics processors.
The current software tools we use are expensive, slow, and generally inadequate. A small amount of money spent by the NIH developing and standardizing these tools would save researchers money, time implementing solutions themselves, and time actually using the programs.