Her titles are different depending on the country concerned. In the UK, which is where she spends most of her time, she's known as Queen of the United Kingdom (although most people just refer to her as Queen of England). In Australia she's Queen of Australia; in Canada she's Queen of Canada, etc.
According to the page in the official website, her title in the UK is "Elizabeth the Second, by the Grace of God of the United Kingdom of Great Britain and Northern Ireland and of Her other Realms and Territories Queen, Head of the Commonwealth, Defender of the Faith".
Looks as though they need a comma after God, though, because at first glance it seems to be saying that God is British. Which he is, of course, but there's no need to brag about it. http://www.royal.gov.uk/output/Page5658.asp
She has separate titles in each of her countries, so when she's in Britain and being Queen of the United Kingdom, she isn't using her Australian or Canadian or other titles; I think this is something of a change from how it was done before. This article is a useful explanation of the history behind the monarch's title:http://www.etoile.co.uk/Columns/Paul/061029.html