Eclipse User:
In Window > Preferences > Run/Debug > Console there's a checkbox "Limit console output" and a textfield for entering the buffer size of the console. However, you can increase it up to 1000000
Eclipse Plugin Development:
To uncheck the console output limit:
IPreferenceStore store = DebugUIPlugin.getDefault().getPreferenceStore();
store.setDefault(IDebugPreferenceConstants.CONSOLE_LIMIT_CONSOLE_OUTPUT, false);
To change only the buffer limit:
store.setDefault(IDebugPreferenceConstants.CONSOLE_LOW_WATER_MARK, 500000);