If you are using python, you need to set the correct paths on Project -> Properties -> External Libraries or edit the .pydevproject file. I did it a few days ago, just replace the ones that can't be found with the ones below.
<pydev_project>
....
<pydev_variables_property name="org.python.pydev.PROJECT_VARIABLE_SUBSTITUTION">
<key>GOOGLE_APP_ENGINE</key>
<value>/usr/Local/google_appengine</value>
</pydev_variables_property>
<pydev_pathproperty name="org.python.pydev.PROJECT_EXTERNAL_SOURCE_PATH">
<path>${GOOGLE_APP_ENGINE}/lib/antlr3</path>
<path>${GOOGLE_APP_ENGINE}/lib/enum</path>
<path>${GOOGLE_APP_ENGINE}/lib/fancy_urllib</path>
<path>${GOOGLE_APP_ENGINE}/lib/google-api-python-client</path>
<path>${GOOGLE_APP_ENGINE}/lib/graphy</path>
<path>${GOOGLE_APP_ENGINE}/lib/grizzled</path>
<path>${GOOGLE_APP_ENGINE}/lib/httplib2</path>
<path>${GOOGLE_APP_ENGINE}/lib/ipaddr</path>
<path>${GOOGLE_APP_ENGINE}/lib/oauth2</path>
<path>${GOOGLE_APP_ENGINE}/lib/prettytable</path>
<path>${GOOGLE_APP_ENGINE}/lib/protorpc</path>
<path>${GOOGLE_APP_ENGINE}/lib/python-gflags/tests</path>
<path>${GOOGLE_APP_ENGINE}/lib/simplejson</path>
<path>${GOOGLE_APP_ENGINE}/lib/sqlcmd</path>
<path>${GOOGLE_APP_ENGINE}/lib/yaml/lib</path>
<path>${GOOGLE_APP_ENGINE}/lib/django-1.4</path>
<path>${GOOGLE_APP_ENGINE}/lib/webapp2-2.5.2</path>
<path>${GOOGLE_APP_ENGINE}/lib/markupsafe-0.15</path>
<path>${GOOGLE_APP_ENGINE}/lib/jinja2-2.6</path>
<path>${GOOGLE_APP_ENGINE}/lib/webob-1.1.1</path>
<path>${GOOGLE_APP_ENGINE}</path>
</pydev_pathproperty>
</pydev_project>