I had a number of recent queries from people, asking me on what to do or where to look for web parts that have suddenly gone missing on thier site pages.

In my experience there are two places one should check:

a) Web parts are treated as any other file in SharePoint and can inherit permissions or have unique item level permissions. Web parts are only visible to users who  have at least read only access to the .webpart or .dwp files in the web parts gallery for the web parts.  Check for change of permissions, including recent removal of  OOTB groups or all authenticated users group (NTAUTHORITY). Also  sometimes SharePoint does not copy (or inherits) top level permissions to the web parts gallery and the _catalog folders so rechecking and manually adding accounts might be required. This is also how you can control the availability of web parts per user or group basis.

b) The second is the use of audiences for web parts, web parts go missing if audiences hace been set for the web parts and they are reset or have not been compiled or one does a restore of a site in a new domain or new SP Farm where the audiences are no longer available.

Note: All other hanky panky like deletion of web part dlls from the web server or removal of safe control entries from the web.config will show an appropriate error message and should not do a houdini.