To index and search through a large collection of PDFs and other document formats, several programs are available. Spotlight in Mac OS X provides built-in indexing and search capabilities. Google Desktop is another option, compatible with Mac OS X, Linux, and Windows, allowing users to search for specific words or phrases within documents. Windows Desktop Search can also perform this function, although it may require the installation of an IFilter for optimal performance. Other desktop search engines may offer similar indexing and searching features, providing various options for users looking to manage and search their document collections effectively.