there are a lot of Real-time PCR methods, such as in EU, Japan, Taiwan, Korea web site, the new technology using NGS tech to analysis GMO, you can see on http://diposit.ub.edu/dspace/handle/2445/32002 and more paper.
Co-Extra was a EU research programme on co-existence and traceability. One of the research themes was on "alternative methods". You may find the following link useful: http://www.coextra.eu/research_themes/topics203.html
You may be also interested in reading "How to reliably test for GMOs" by Zel et al. (See http://www.springer.com/food+science/book/978-1-4614-1389-9 ) or you may wish to have a look at the reference methods listed on the website of the European Reference Laboratory for GMOs: http://gmo-crl.jrc.ec.europa.eu/gmomethods/
These are just appetizers; there is plenty of stuff directly available on the web.
The difference between a GMO and a non-GMO is a specific piece of DNA and the protein it encodes. Therefore, any method to detect GMOs would typically rely on finding that specific DNA or protein. Methods will be product-specific, so other ways may be possible depending on the GMO trait. Are you looking for a specific GMO?