God of the Gaps is a concept that comes from the fact that God is being squeezed into an ever smaller series of existential gaps.
At one time, all the phenomena in the universe could be ascribed to a god or gods, phenomena such as the stars, the rain, the seasons etc. With time, and improved scientific explanations, the number of things for which "God did it" was a good explanation was reduced, and god was equally reduced to inhabiting ever smaller gaps in human knowledge.
Less well-educated theists still try to use God to explain a vast number of things, but better-educated believers now only bring God up to try and explain things where science has no generally agreed explanation. Two popular god-gaps are the initial formation of life, where believers churn out material full of logical fallacies, and the Origin of the Universe, where there are similar fallacies.
While there are a number of hypotheses about both these issues, it is difficult to say that there is a comprehensive scientific consensus - and so they are to convenient gaps where the religiously-minded can insert their deity or deities of choice.
It should be remembered however, the fact that science has no present explanation in no way means that god (or Uranus, Zeus, Odin or any other god/goddess) exists or that the God/Gods of any other Mythology exist. Indeed, if we were never to answer these questions it still wouldn't mean that Allah created the Universe or that Thor causes it to thunder.
- Baba Brinkman – God of the Gaps A cool song with cool pictures explaining God of the Gaps