What is still missing in Sharepoint ? -
Time - Tracking - to do PSA: (Professional Services Automation) - time tracking, billing .... even a basic object would be fine -
Org Chart Wizard: most customers don't know how to structure a Sharepoint installation, most often they don' t have all the needed info in Active Directory. Therefore having some sort of wizard to create an org chart - will all business units, departments and "workgrups" which generates a structure within MOSS would be ideal, especially when done and validated by a HR person
Anything else?
Sharepoint Taxonomy