We present a reproducible method to analyze the state of software development practices in a given scientific domain and apply this method to Geographic Information Systems (GIS). The analysis is based on grading a set of 30 GIS products using a template of 56 questions based on 13 software qualities. The products range in scope and purpose from a complete desktop GIS systems, to stand-alone tools, to programming libraries/packages. The final ranking of the products is determined using the Analytic Hierarchy Process (AHP), a multicriteria decision making method that focuses on relative comparisons between products, rather than directly measuring qualities. The results reveal concerns regarding the correctness, maintainability, transparency and reproducibility of some GIS software. Three recommendations are presented as feedback to the GIS community: 1) Ensure each project has a requirements specification document, 2) Provide a wealth of support methods, such as an IRC (Internet Relay Chat) channel, a Stack Exchange tag for new questions, or opening the issue tracker for support requests, as well as the more traditional email-based methods, and, 3) Design product websites for maximum transparency (of the development process), for open source projects, provide a developer's guide.