Im a bit uncertain about when to apply for indefinite leave to remain for the missus especially so because of recent changes. My Wife got her spousal visa issued 26/06/2011 and we arrived in the UK 15/07/2011, the thing that Im not sure about is that she went back to Thailand to see her family 02/08/2012 until 02/09/2012 and Im not sure how this affects the timing of the ILR application.

Any advice would be welcome.

that length of time out of the uk doesnt affect it at all so you can apply 28days before the 2yr anniversary she entered the country up to the date her visa expires.

Indeed.

See also this topic.

Thanks very much