By default, the Eclipse application is launched with all the workspace plug-ins and all the plug-ins selected on the Plug-in Development > Target Platform preference page.
It is possible however to hand-select a subset of plug-ins to launch with on the Plug-ins tab of the launch configuration.
This gives you great flexibility, but with flexibility comes the danger of ending up with an invalid configuration. Use this feature carefully and press the Validate Plug-in Set often to ensure that all inter-plug-in dependencies in your subset are satisfied.