The former means application of genetics, while second implies selective breeding.
I've honestly got nothing against GMO, and I know that GMO carries a stigma, but honestly, so do vaccines. I've got loads of problem with Monsanto, their business practices and Round-up but not too many problems with GMO as GMO.
The so-called "traditional" method of crop development, on the other hand, takes genes not just from other creatures but from totally random mutations, often induced by carcinogens and radiation, and then selected.
With GMOs we know much more about what has happened to the genome of the species.
I think even regular GMO technology probably still is affected by radiation (cosmic radiation and sun) and breeding - I doubt every single grain of corn is genetically manufactured once you can just let it naturally breed.
Not to mention radiation is a great and cheap way to rid of some pests really fast, but tell that to any organic food lover and they'll get defensive.
http://ideonexus.com/2011/12/05/gmo-foods-and-the-promise-a-...