have a look at the automatically created project "servers". there should be a folder for each configured server. there, open the context.xml and add anything you like to be in the "default" context (parameter-tags for example).
anything that's inside there will be used to populate the context.xml wtp automatically creates on publishing for each project on that server.
or use the project specific way: put a context.xml with your contents inside meta-inf in your project (have a look here: http://wiki.eclipse.org/wtp_tomcat_faq#how_do_i_specify_the_tomcat_context_configuration_for_my_web_application.3f)
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