You should be able to build a particular version of your Mule project at any point of time. This facilitates maintenance as the versions of your projects in production will certainly not be the latest ones.
The following will help you achieve this goal:
Source control all your Mule project, like any other project (remember not to check-in Eclipse specific files). Branching, merging and tagging are all applicable practices to Mule projects
Manage dependencies strictly: using Maven and an in-house repository manager (like Nexus) will get you a long way there.