You should be able to build a particular version of your Mule project at any point in time. This facilitates maintenance, because the versions of your projects in production are not always the latest ones.
To help achieve this goal:
Use source control for all your Mule projects and apply branching, merging, and tagging to them. (Do not check in Eclipse-specific files.)
Manage dependencies strictly by using Maven and an in-house repository manager, such as Nexus.