[HD2 Windows Mobile 6.5 ROM Development] appelflap:
Remove (or uncheck) the packages and edit the 26948339_manila file in the Manile Core directory:

<Manila Mode9Path="HTC\Manila\manila.mode9">
<Navigation>
<PageGroup Name="Root">
<Page Order="0" Name="home.page" PackageName="HTC" Default="true" Title="[[IDS_HOMETITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\Home\FakeHome.mode9?testParam=1" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Home_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Home_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Home_Preview"/>
</Page>
<Page Order="1" Name="people.page" PackageName="HTC" Title="[[IDS_FAVORITEPEOPLETITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\People\people.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="People_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="People_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="People_Preview"/>
</Page>
<Page Order="2" Name="messaging.page" PackageName="HTC" Title="[[IDS_MESSAGESTITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\Messaging\messaging.mode9" Component="MessagesTopLevelPage" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Messaging_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Messaging_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Messaging_Preview"/>
</Page>
<Page Order="3" Name="email.page" PackageName="HTC" Title="[[IDS_EMAILTITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\Email\email.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Email_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Email_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Email_Preview"/>
</Page>
<Page Order="4" Name="internet.page" PackageName="HTC" Title="[[IDS_INTERNETPORTALTITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\Internet\internetportal.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Internet_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Internet_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Internet_Preview"/>
</Page>
<Page Order="5" Name="reader.page" PackageName="HTC" Title="Reader">
<ComponentReference Name="page" Mode9Path="HTC\Reader\Reader.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Reader_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Reader_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Reader_Preview"/>
</Page>
<Page Order="6" Name="album.page" PackageName="HTC" Title="[[IDS_PHOTOSANDVIDEOS]]">
<ComponentReference Name="page" Mode9Path="HTC\Album\album.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Album_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Album_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Album_Preview"/>
</Page>
<Page Order="7" Name="music.page" PackageName="HTC" Title="[[IDS_MUSICTITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\Music\music.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Music_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Music_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Music_Preview"/>
</Page>
<Page Order="8" Name="calendar.page" PackageName="HTC" Default="true" Title="[[IDS_CALENDAR]]">
<ComponentReference Name="page" Mode9Path="HTC\Calendar\Calendar.mode9" Component="CalendarComponent" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\CalendarIcon.mode9" Component="Calendar_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\CalendarIcon.mode9" Component="Calendar_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\CalendarIcon.mode9" Component="Calendar_Preview"/>
</Page>
<Page Order="9" Name="inforwidget.page" PackageName="HTC" Title="[[IDS_STOCK]]">
<ComponentReference Name="page" Mode9Path="HTC\Stock\infor.mode9?page=MyPortfolio" Component="DetailPage" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\inforicon.mode9" Component="infor_tray_icon"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\inforicon.mode9" Component="infor_tray_icon_selected"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\inforicon.mode9" Component="infor_tray_icon_preview"/>
</Page>
<Page Order="10" Name="footprints.page" PackageName="HTC" Title="[[IDS_FOOTPRINTS_TITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\Footprints\footprints.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\Footprints_icons.mode9" Component="Footprints_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\Footprints_icons.mode9" Component="Footprints_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\Footprints_icons.mode9" Component="Footprints_Preview"/>
</Page>
<Page Order="11" Name="docexplorer.page" PackageName="HTC" Title="[[IDS_DOCUMENTSTITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\DocExplorer\documentexplorer.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\DocExplorer\docicons.mode9" Component="DocumentExplorer_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\DocExplorer\docicons.mode9" Component="DocumentExplorer_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\DocExplorer\docicons.mode9" Component="DocumentExplorer_Preview"/>
</Page>
<Page Order="12" Name="twitter.page" PackageName="HTC" Title="[[IDS_TWITTER]]">
<ComponentReference Name="page" Mode9Path="HTC\Twitter\Twitter.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Twitter_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Twitter_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Twitter_Preview"/>
</Page>
<Page Order="13" Name="weather.page" PackageName="HTC" Title="[[IDS_WEATHER]]">
<ComponentReference Name="page" Mode9Path="HTC\Weather\weather.mode9" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Weather_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Weather_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Weather_Preview"/>
</Page>
<Page Order="14" Name="MyplaceApps.page" PackageName="HTC" Title="Apps & Downloads">
<ComponentReference Name="page" Mode9Path="HTC\Myplace\myplace.mode9?config=windows\programitems_AD.xml&reg=AD" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\telstraicon.mode9" Component="Downloads_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\telstraicon.mode9" Component="Downloads_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\telstraicon.mode9" Component="Downloads_Preview"/>
</Page>
<Page Order="15" Name="MyplaceTV.page" PackageName="HTC" Title="TV">
<ComponentReference Name="page" Mode9Path="HTC\Myplace\myplace.mode9?config=windows\programitems_TV.xml&reg=TV" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\telstraicon.mode9" Component="TV_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\telstraicon.mode9" Component="TV_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\telstraicon.mode9" Component="TV_Preview"/>
</Page>
<Page Order="16" Name="MyplaceNews.page" PackageName="HTC" Title="News and Sport">
<ComponentReference Name="page" Mode9Path="HTC\Myplace\myplace.mode9?config=windows\programitems_NS.xml&reg=NS" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\telstraicon.mode9" Component="News and Sport_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\telstraicon.mode9" Component="News and Sport_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\telstraicon.mode9" Component="News and Sport_Preview"/>
</Page>
<Page Order="17" Name="MyplaceSocial.page" PackageName="HTC" Title="Social Web">
<ComponentReference Name="page" Mode9Path="HTC\Myplace\myplace.mode9?config=windows\programitems_SW.xml&reg=SW" Component="GizmoRoot" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\telstraicon.mode9" Component="Social Web_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\telstraicon.mode9" Component="Social Web_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\telstraicon.mode9" Component="Social Web_Preview"/>
</Page>
<Page Order="18" Name="settings.page" PackageName="HTC" Title="[[IDS_SETTINGSTITLE]]">
<ComponentReference Name="page" Mode9Path="HTC\Settings\settings.mode9" Component="SettingsPageComponent" SmartComponent="true"/>
<ComponentReference Name="icon_normal" Mode9Path="HTC\Manila\icons.mode9" Component="Settings_Off"/>
<ComponentReference Name="icon_selected" Mode9Path="HTC\Manila\icons.mode9" Component="Settings_On"/>
<ComponentReference Name="icon_preview" Mode9Path="HTC\Manila\icons.mode9" Component="Settings_Preview"/>
</Page>
</PageGroup>
</Navigation>
</Manila>
[/SIZE]

Remove the page-nodes that correspond to the packages you want to delete, fix the pagenumber ordering and you are all done.

BTW the settings page can't be deleted without loosing some hometab menu functions. Also, if you remove the weather page the clock and alarm page won't work anymore :confused: