One somewhat annoying thing about running JUnit tests in Eclipse is that they do not inherit your system's environment variables. There are good reasons for this, but we pass our AWS credentials to all of our applications via system variable, and it's a pain to add these to every single run configuration that needs them. This gets especially tedious when a significant number of your JUnit tests require AWS access.
As a workaround, you can add "Default VM Arguments" to the JVM you use to run your tests. Simply go to "Preferences->Java->Installed JREs" and edit your default JVM. Right under the JRE name is a space to add default VM arguments. I simply added "-DAWS_SECRET_ACCESS_KEY=foo -DAWS_ACCESS_KEY_ID=bar", and now I no longer need to manually edit individual run configurations.
This method seems a bit hacky to me, but until I can get a global run configuration, it definitely beats manually setting common environment variables for individual tests.