You want to enable assertions for an application you're running from Eclipse? I usually just add -ea to the command line parameters in the "Run As" profile.
If you want to solve this issue globally for all JUnit tests then go to Preferences > Java > JUnit and at the top click the checkbox for "Add 'ea' to VM arguments when creating new JUnit launch configuration" Now Eclipse won't bug you for every new test you want to run. For existing tests you have to remove their's run configurations in Run Configuration > JUnit.
To do this globally for all Java runs, edit the Installed JREs properties.
For example: Windows -> Preferences -> highlight the default JRE -> click Edit... -> In the Default VM arguments input box, enter -ea -> click the finish button.