Is this site elsewhere, or is it your site? If you are searching on your site then you can use the Index Server to search through the documents. If it's on a different server then you will have to adopt a more brute force approach.
With the brute force approach, you will need to copy the document onto your system and then use the IFilter COM API to get the text from the document. Have a look at
this[
^] article for more detail on how to use it.