Yes you can use Indexing Service to search, but yu should be aware that
by default the filter for pdf documents and office documents are not
installed on the indexing service hence it will not be able to search
for text inside these documents. The filters get installed only when the
 corresponding apps are installed i.e. (Adobe Acrobat or Reader and MS
Office)

To see how you can use the Indexing Service from your .Net application
check out this article
http://idunno.org/dotNet/indexserver.aspx

It's for ASP.Net but the code code remains the same.

Btw i also came across this while researching
http://www.copernic.com/en/products/desktop-search/
seems nice :)

Sijin Joseph
http://www.indiangeek.net
http://weblogs.asp.net/sjoseph