The default tool suite (i.e. the tools added to a site on creation) is specified in the file toolOrder.xml file (located in the .../apache-tomcatxxx/sakai folder).
See the sample extract from the toolOrder.xml file for course sites below:
<toolOrder><category name="course">
<tool id="sakai.iframe.site"/>
<tool id="sakai.synoptic.chat"/>
<tool id="sakai.synoptic.announcement"/>
<tool id="home" selected="true"/>
<tool id="sakai.announcements" selected="true"/>
<tool id="sakai.schedule"/>
<tool id="sakai.syllabus"/>
<tool id="sakai.resources" selected="true"/>
<tool id="sakai.lessonbuildertool" selected="true"/>
<tool id="sakai.podcasts"/>
<tool id="sakai.rwiki"/>
<tool id="sakai.poll"/>
<tool id="sakai.messagecenter"/>
<tool id="sakai.forums"/>
<tool id="sakai.messages"/>
<tool id="sakai.discussion"/>
<tool id="sakai.mailbox"/>
<tool id="sakai.chat" selected="true"/>
<tool id="sakai.dropbox"/>
<tool id="sakai.assignment.grades" selected="true"/>
<tool id="sakai.samigo"/>
<tool id="sakai.gradebookng" selected="true"/>
<tool id="sakai.postem"/>
<tool id="sakai.news"/>
<tool id="sakai.iframe"/>
<tool id="sakai.sections"/>
<tool id="sakai.site.roster" selected="true"/>
<tool id="sakai.search" selected="true"/>
<tool id="sakai.siteinfo" selected="true" required="true"/>
</category><category name="project">
The tools which include selected="true" will be selected by default when the person creating the site is on the Site Info > Edit Tools > Course Site Tools screen.
The tools which include required="true", such as Site Info, are mandatory tools. The user will not be able to de-select them on the Site Info > Edit Tools > Course Site Tools screen.
If your instance of Sakai uses different site types (project, collaboration etc.), each site type can its own section in the toolOrder file.