This is a loaded question as there is probably not one single answer for everyone. There are important considerations, however, that do apply to all. I have earned a living for the past 14 years as a GIS/Database specialist for a number of small but growing environmental consulting firms. This post is specific to my experience but I suspect that at least some aspects of it are common to small consulting firms in other fields and possibly small non-profits as well. I will focus specifically on optimizing the GIS data storage of large datasets in a single-user environment with this post, but I will follow shortly with a second post dealing with moving from single user desktop GIS to multi-user enterprise level systems.
Questions and answers about common geospatial issues.