The thing about non-enterprise data storage is the users of this data frequently have changing/varying needs. In an enterprise setting it's not always most efficient to store data in central geodatabases, but it goes a long way in sticking people to standards, which can be taught and monitored.
At the most basic level, a small company should house any "universal data" in a globally accessible (in terms of the organization) place. For example, if the company works mainly within one state/province they would store all state-wide base layers on a server. Any common edits (clipped regions) would be stored in sub-folders/geodatabases.
The next level of data storage (personal) can go a few ways. If many people work on a single project they may need to store their data on the same globally accessible server. If only one person is working on the project a local storage solution (backed up!) is fine. How this is done would be up to the individual user, but I think it's safe to say a common solution would be to use individual project folders, possibly containing geodatabases, depending on the project specifics.
Edit: If we're talking about a single user, the same general idea applies. Instead of housing global data on a server, they would use a separate drive/partition/sub-folder.
