I’ve noticed that many nonbelievers (and even believers) misunderstand what constitutes a “God of the gaps” argument. They tend to think one is guilty of a God of the gaps argument if they offer God as an explanation for some X rather than some natural phenomenon. The problem with this definition is that it presumes the only valid explanation is a naturalistic explanation. God is ruled out as a valid explanation for anything a priori, so anyone who offers God as an explanation for X is thought to do so merely because they are ignorant of the proper naturalistic explanation. This begs the question in favor of naturalism and against theism. One could only conclude that every effect has a naturalistic explanation, and that God is not a valid explanation, if one has first demonstrated that God does not exist. So long as it is even possible that God exists, then it is possible that God may be the cause of X, and thus explain X.
What makes an argument a God of the gaps type of argument is when God is invoked to explain X simply because we do not know what else can explain X. In other words, God is used to plug a gap in our knowledge of naturalistic explanations: “I don’t know how to explain X, so God must have done X.” This is not at all the same as arguing that God is the best explanation of X, based on what we know regarding X and the explanatory options available to us. Here, God is being invoked to explain what we know, not what we don’t know.