I've noticed a pattern here (I'm sure I'm not the first, though). We all know that we are not omniscient- none of us knows everything. Which means that everyone has gaps in their knowledge, and we fill those gaps with something (there are no exceptions, as I am about to show). As mentioned in my previous posts "What is Faith?" and "Do You Rely on Authorities?" we tend to look to past experiences to determine what to put our trust in to fill those gaps.
Theists find that God is a trustworthy source, so they fill those gaps with God. This can be both good and bad. The big accusation that comes mainly from the scientific community is that when God is placed in a gap in knowledge, then the person is intellectually satisfied and refuses to investigate further. I can't deny that in many cases, this is true. Some people permanently fill the gaps with God- they do not allow for the gap to be filled by something else, when it is perfectly acceptable (these opportunities arise as research into the natural realm progresses). This is academically dishonest. However, the other side cannot deny that even though God is in a gap, investigation continues and may even spur more investigation (the thing that comes to mind is Junk DNA- see Chapter 13 of Dr. Hugh Ross' book "More Than a Theory" for this). God is a possible explanation of the gaps of knowledge, so He is perfectly acceptable in a theistic worldview. The only time this becomes unacceptable is when theists refuse further investigation, and this is really not all that common.
On the non-theistic side of the coin, several gap-fillers exist also: Naturalism, Epistemological Uncertainty, and Epistemological Impossibility (all- "...-of-the-gaps", if you will).
Naturalism-of-the-gaps is simply faith (trust) of the skeptic that naturalism will be able to explain the gaps of knowledge based on the past experience with naturalism explaining other gaps in knowledge. Like God-of-the-gaps, naturalism is put in the gap of knowledge prior to investigation. However, unlike God-of-the-gaps, naturalism is not always a possible explanation. For instance, naturalism cannot explain the existence of non-physical entities, such as laws of logic. Many naturalists still place naturalism in the gap, because they do not like one of the alternatives (to be fair, many theists do the same thing)- be it some god or something else that is metaphysical. This is academically dishonest and betrays an emotional commitment to an idea despite the evidence. Oddly enough, science assumes the laws of logic before it can be exercised. Since it must be assumed, it is not within the realm of science to prove or disprove- something metaphysical must be posited by the naturalist to ground the law of logic before science can even take place. The only explanation they provide is "...well, its NOT God!" Yet they don't provide evidence for some other entity, they just remove God from possibility and leave an epistemic void which is supposed to ground the very science they say is so solid.
Another option for a gap-filler is epistemological uncertainty, or simply "agnosticism" ("there is not enough evidence to decide"). This is not really based on previous experience with agnosticism, but experiences with both theism and naturalism. Agnostics believe that a knowledge gap can be filled by either. However, a suspension of conclusion is still a position, nevertheless. The gap has been filled, but not satisfactorily. Now, I have run into many people who claim agnosticism even after evidence one way or another becomes available, yet they continue to "fill" the gap with agnosticism. It seems that "agnosticism" is a public position, while they privately have filled the gap, and if that filler is not affirmed, they hold the "agnostic" position in public to avoid criticism of their view or appearing to hold a view against the evidence (this goes for both theistic and non-theistic sides).
The fourth possible gap-filler is epistemological impossibility or "mystery". I see this all the time. It is normally the result of the continued failing of one of the other three, but refusal to accept the one the person is opposed to. These people simply take the position that it is impossible to fill a gap in a theistic or non-theistic way. They are not saying that the gap is not filled in reality, just that it is impossible for us to know what fills the gap. This is not, however, always academically dishonest. Any worldview that posits the existence of something that cannot be directly tested by humanity (typically metaphysical) will include some level of mystery. But any worldview that posits the existence of only that which is directly testable by humanity (not metaphysical) does not have room for this position on a permanent basis.
Who Uses Which Gap-Filler?
Even though the final three are the only options available for many non-theists (but not all non-theists), all four are available for the theist. Nature can fill knowledge gaps in a theistic worldview (see Chapter 3 of "More Than A Theory"); so can mystery. A theistic worldview is allowed to follow the evidence where it leads; it is not limited by a prior commitment to a non-theistic universe. If the most reasonable explanation for a phenomenon is an intelligent source, and man has been eliminated as a possibility, then we have an Intelligent Being that is not man that we can appeal to to explain the phenomenon. If the most reasonable explanation for a phenomenon is a natural process, we have all the same natural processes that the naturalist possesses to appeal to to explain the phenomenon.
Not only that, we must remember that just because theists state that a phenomenon takes place via natural processes or laws, that does not necessarily mean that God is NOT behind it. Obviously, theists believe that God created everything. Much like a manufacturing plant, the end product is the product of dumb machinery, but it reflects the design of an original template that is the product of an intelligence (let's not forget the machines are the product of a design created by an intelligence also). Hence, just because we attribute a final product to a natural process, does not mean that we attribute the natural process to randomness- the process is also the result of an intelligent designer- thus so is the finished product. The source of the original blueprints or schematics of the end product ready for consumption is the product of an intelligence. In nature we see similar (and even more complex than humans have produced) products and systems. By analogy it is perfectly reasonable to conclude that a mind is behind the original blueprints and schematics of those phenomena.
For obvious reasons God is not an available gap-filler for the atheist, so of the list, they only have three options: Nature, Uncertainty, and Mystery are all available. Typically, nature is the most commonly used; however, a gap may not be able to be filled with anything natural, and in that case, uncertainty or mystery may be used.
Please recall the discussion above about naturalism. The insistence that the gap in knowledge be "NOT God" still leaves a gap. Since naturalism is not an option, only uncertainty and mystery are available as gap fillers. Rather than allow for the third option that is available to the theist, the atheist will prefer either to not take a position (uncertainty) or state that it is a mystery that we will not be able to discover.
Unfortunately, "for some, winning matters more than anything, and consequently they go to great lengths to find the just-right tactic, regardless of whether it advances the search for truth."  Anytime we place our trust in something to fill a gap in our knowledge, we exercise faith. We use something-of-the-gaps argumentation. When we realize that everyone exercises this argumentation, we can have conversations and dialogues that are much more constructive and will advance the search for truth. Accusing one side of "gaps" argumentation while refusing to acknowledge that we (theist, atheist, or agnostic) exercise the same is dishonest and, some would say, "hypocritical".
This is one of the most powerful ways to test a worldview (or religion). With exactly what we fill knowledge gaps is an indicator to the truth of our worldview. If we take a stand on what our view states will fill a knowledge gap, we are essentially making predictions about what humanity will discover about reality. The gap-filler can be tested. With each affirmed prediction, that worldview is verified to accurately reflect reality. With each failed prediction, that worldview is falsified for accurately reflecting reality- adjustment is needed or abandonment may be in order...but don't be tempted to appeal to mystery when the evidence points to another view already on the table.
Referring to the "new atheists", Ravi Zacharias states this: "They are not open or willing to go where the evidence leads, unless that evidence sustains their own naturalistic assumptions. They have covertly reduced all philosophical thought and deduction to-- ironically-- faith" (emphasis in original) 
- Dr. John Lennox speaks to the issue of "God-of-the-gaps" argumentation in a talk found here.
- Stephen McAndrew looks at the idea that God was invented to fill in gaps in the knowledge of ancient humans in his post Divine Invention.
- Do You Rely On Authorities?
- The Validity Of The Process of Elimination
- What Is Faith?
- Book Review: More Than A Theory
 Dr. Hugh Ross- "More Than A Theory: Revealing a Testable Model for Creation" pg 35
 Dr. Ravi Zacharias- "Has Christianity Failed You" pg 51