Greg Beaver has written an interesting set of ten golden rules for running open source projects. Many of these rules apply to running (or working on) anything. My favorite rule is "3. Despite the evidence, it's probably your fault." Greg develops the popular Open Source project PEAR, a packaging tool for PHP that looks similar in concept to RubyGems.
Cheminformatics, like all vertical markets, has is own peculiarities when it comes to Open Source. Most importantly, cheminformatics software has a limited, but captive audience. When done well, it is both highly profitable and expensive to develop. For insightful perspectives on Open Source software as it applies to cheminformatics and vertical markets, see Matt Stahl, Warren DeLano, Craig James, and Eric S. Raymond.