I'll preface this by saying that I usually work in C#/.Net.
Normally, I use a naming scheme that puts common, reusable components into a namespace that reflects our organization and project-specific components into a namespace tied to the project. One of the reasons I do this is that I sometimes share my components with others outside my department, but within the organization. Project-specific namespaces are typically prefaced with the name or abbreviation of the department. When I reuse code between projects, I typically migrate it into one of the organization-based namespaces.
For example:
UIOWA.DirectoryServices
contains classes that deal with the specific implementation of our Active Directory.
UIOWA.Calendar
contains classes that deal with the University's master calendar.
LST.Inventory.Datalayer
holds the classes implementing the data layer of the Learning Spaces Technology group inventory application.
I'm embarking on a project now for an entity that has a fuzzier connection to the Unviersity (a student group that runs a charity event) that has the potential to be sold outside of our University and, thus, it doesn't really fit into my normal naming conventions, i.e., the department is only the first customer of potentially many that might use the project.
My inclination is to go the organization naming route and create an "organizational project" name space for this application. I'd like to hear how others handle this and any advice you might have.
Thanks.
See also this related question about namespace organization.
EDIT
I ended up creating the org/project namespace UIOWA.MasterEvent
and deriving further namespaces from there. Still interested in other opinions for future projects.