How did a small prop plane get from Nigeria to the South Pacific?
It flew over the spot in Tunisia where you get dumped if you turn the donkey wheel, maybe? Needs to be explained, though.

How did backwards-talking Walt appear to Shannon, how did he know the information he provided (about the Hatch button, and people who are coming), and why does he talk backwards? Were these just visions in Shannon's head (we can assume no, since Sayid does see him, too), or was Walt somehow projecting himself to her?
Now that we now more about the themes of mirrors/reflections in the show, does that have something to do with the backwards talk? We also saw Locke show up inexplicably wet one time (the time he blew up the sub). Another question: why did Walt (in backwards speak) warn them about pressing the button (he said it was "bad"), when we know the button was good and it was most certainly necessary to press it? Unless of course what happened (such as Desmond's new powers) was what needed to happen as a result of the Swan implosion.

Did Ben intentionally get caught in Danielle's trap?
This one's open for interpretation. Whether Ben meant to get caught or not, he used it to his advantage toward his goal of infiltrating the 815ers.

Why did the Others want baby Aaron? Was it only to do with their conception issues, or was it something more specific about him?
Did they perhaps receive a list from Jacob with the directive to acquire Claire's baby?

How is it that Dharma is still dropping food and supplies on the island in 2004, so many years after the Purge? How do they do it (we saw how difficult it was for Faraday & Co. to parachute in)?
Was the food drop dropped in another time period and it landed in this one? Is it even an air drop at all, or just staged by the Others to look like one?
Related Question: Why is Ben's refrigerator full of Dharma food products? Where do they keep coming from? Why does Dharma continue to ship food if Ben & the Hostiles wiped them out? Don't they realize nobody is doing their projects?
Seriously, this has bugged me for a long time, and I'm fresh outta theories on why Dharma products continue to show up in 2004.

Libby Stuff: What was Libby doing in Santa Rosa? Will Hurley ever figure out where he knew her from? What is her last name? Did someone send her to "coincidentally" meet Desmond and offer him her boat The Elizabeth for his race?
We'll see Libby at some point in the new-815 Side-Verse. There's always been plentiful speculation that she's a Widmore or worked for him. And if you consider her roles in the lives of the very-important Hurley and Desmond, was she perhaps an Abaddon-like personage?

Who is the "great-but-unforgiving man" Ben once told Locke was "in charge"?
Here were my musings on that back at Milepost 11 of our journey: "The man in charge, John, he's a great man, a brilliant man. But he is not a forgiving man. He'll kill me because I failed." -- Ben, to Locke. So, here's the thing: on one level Ben is talking about himself, in which case this would be filed under Characterization - Ben is unforgiving and does not tolerate failure. On another level, it sounds as if he's talking about some sort of god, but definitely not THE God that I know. Sounds more like his counterpoint Satan. On yet another level, he could be speaking of either Jacob, or even possibly the Man in Black. It's a statement I still haven't figured out."

Why does a captive Ben say the line, "God can't see this island"?
We know the island is invisible because it has probably moved just barely ahead in time in relation to anyone looking for or observing the spot where it's supposed to be. But come on, if migratory birds can find it, so can God. Unless this is a clue to it being so far removed from God (i.e. the Hell / cork keeping Hell bottled up metaphors of our most recent episode) that it's beyond His care or observation.