Depends on the search engine. Windows Live and Yahoo! both provide
SOAP search APIs, which would be designed specifically for use with
server-side and/or standalone applications. However, Google
deprecated their SOAP search API in late 2006, and has yet to
introduce a replacement. You can vote for server-side access on the
Features Request page.
All of the major search engines frown on "screen scraping" techniques
whereby you submit a query to their regular web interface and then
parse the returned page for information.