Here is the scenario: you have SharePoint 2007 site with search center as a part of it and you have been asked to integrate company`s document management system with sharepoint search. In other words, your document management system has to be searched as any other source and results returned within your search center with relevant webparts.
In this case you will need to implement MOSS 2007 protocol handler allowing for the external data to be crawled and indexed and be searchable within your site.
Protocol Handlers are COM components, usually written in C. .NET allows you to create a class library and expose it as a COM component. Therefore, it is possible to create a .NET COM component which will be consumed by the SharePoint search engines Filter Daemon.
There is a great sample at codeplex not only showing the structure of the protocol handler but also with accompanying sample for docx files and installer. It`s a great starting point for you to implement your handler.