Searching internal documents is not working. The search service indexes all the documents ok, no errors in the logs etc but no results are displayed

Check the alternate mappings as this usually is the issue. For example if the default mapping is http://sitename.companyname.com/sites/sitename1 it would index but not display the results. Changing the default value to http://server (which is the server name of the MOSS web server) and the Extranet mapping to http://sitename.companyname.com/sites/sitename1 then the results will be displayed.

Team Collaboration lists such as Calendar, Tasks lists are unavailable within moss publishing site - How do i fix this?

Very Simple - Goto Site Settings > Site Administration > Site Features and Activate the "Team Collaboration Lists" feature

An error occurred during the compilation of the requested file, or one of its dependencies. The type or namespace name 'Publishing' does not exist

As simple as this error sounds - "An error occurred during the compilation of the requested file, or one of its dependencies. The type or namespace name 'Publishing' does not exist in the namespace 'Microsoft.SharePoint' (are you missing an assembly reference?)", it can be tricky to solve.

The easiest solution I have found to solve is to include the following snippet below your includes in your master page.

<%@ Register Tagprefix="PublishingWebControls" Namespace="Microsoft.SharePoint.Publishing.WebControls" Assembly="Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" %>

<%@ Register Tagprefix="PublishingNavigation" Namespace="Microsoft.SharePoint.Publishing.Navigation" Assembly="Microsoft.SharePoint.Publishing, Version=12.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c" %>

<%@ Register TagPrefix="PublishingVariations" TagName="VariationsLabelMenu" src="~/_controltemplates/VariationsLabelMenu.ascx" %>
<%@ Register Tagprefix="PublishingConsole" TagName="Console" src="~/_controltemplates/PublishingConsole.ascx" %>

<%@ Register TagPrefix="PublishingSiteAction" TagName="SiteActionMenu" src="~/_controltemplates/PublishingActionMenu.ascx" %></strong>

How to fix the issue "A feature with ID ... has already been installed in this farm. Use the force attribute to explicitly re-install the feature."

Use -force flag on your deploy operation. For example:

stsadm -o deploysolution -name MyBranding.wsp -immediate -force
stsadm -o execadmsvcjobs
stsadm -o activatefeature -name Mybranding -url http://testurl -force