To be honest, this is mostly clarification for myself, just because even though you can watch and rewatch Lost millions of times, it's still damn confusing. To me, one of the most confusing things is not the questions, but the answers. This isn't a show like 24 or Flashforward, in which everything can be explained rationally and scientifically; it's also not all based on supernatural beings and powers like Heroes; rather, it's a mix of both, in which questions are answered by different means. For instance, we know that Locke's paralysis was healed by the island, but that doesn't really give us any insight; was it Jacob, was it the electromagnetism, or was it just fate resolving itself? Either way, I'm going to try to go through as many mysteries as possible and conclude whether or not they are supernatural, scientific, destiny, or a mix of both. Obviously this will be slightly opinionated, I will try to clarify whenever my conclusions are based on assumptions.
Island's Healing Properties - Supernatural/Scientific
- The combination of Jacob's power and the island's electromagnetic properties seem to heal people; I would suggest that Jin's fertility was by the elecectromagnetic properties of the island, whereas Locke's use of his legs was Jacob's doing. I think it's safe to assume that both supernatural and scientific aspects come into play, and that (this is my own thought) perhaps Jacob uses his powers to 'channel' the electromagnetic deposits.
Whispers - Supernatural
- Though we haven't learned much, it's safe to assume that they are at least partially connected to the Others, from instances such as when Harper appears and disappears from Juliet; by extension, they would then be connected to Jacob. Of course, Harper may have been a manifestation from the monster, which would then connect the whispers to the Man in Black. Either way, they seem to be a supernatural occurence.
The Numbers - Scientific/Destiny
- Though I never was a part of The Lost Experience, after reading about it I'm under the impression that there was a scientific explanation for the Numbers, or The Valenzetti Equation, and that one of the goals of Dharma was to in fact attempt to manipulate them. However, this doesn't explain why they seem to show up constantly in Hurley's life, or why they appear everywhere. I wouldn't go so far as to say that they are supernatural, but instead follow the words of Eko: "Do not mistake coincidence for fate."
Hurley Bird - Supernatural (kind of)
- I don't think we'll ever get an explanation of this weird mystery, but if it is in fact significant, I would suggest that it's not scientific or fateful. I've seen many blogs around here throwing around the idea that the Hurley Bird is a manifestation of Jacob or MIB, in which case it would fall under the 'supernatural' category.
Swan Station and Discharge - Scientific
- We've never seen any indications that Jacob, MIB, or any other supernatural beings are related to Dharma's electromagnetic experiments and consequences. We've had a pretty thorough scientific explanation thanks to Desmond, Kelvin, and Faraday.
Pregnancy Issues - Scientific/Supernatural
- Though we've seen scientific and medical experiments, treatments, and studies on why women can't seem to give birth on the island, we've yet to have an explanation. Ironically, the 4-toed statues is actually Tawaret, the goddess of fertility. Is it somehow part of Jacob's or MIB's plan to prevent offsprings on the island, or is it symbolic that the statue was destroyed and now women can't get pregnant? I'm going with supernatural powers using scientific means.
The Sickness - Scientific
- Though there is no indication that there actually is a sickness, I like to assume that it's not related to destiny or the supernatural. Like the Hurley Bird, I think this is one mystery that hasn't been, and won't be, solved.
Sayid's (and possibly Claire's) Resurrection and 'Claiming' - Supernatural
- I think we can all agree that this has nothing to do with science; I think it's obviously MIB's work, and unless there is a scientific explanation for a century-old, shape-shifting smoke monster, this falls under the supernatural category.
Time Travel - Scientific/Destiny
- Though it's not your every day occurence, I think the writer's went to a lot of work to try to explain that there is a scientific explanation for the island travelling through time (why else is Faraday on the show, really?). However, I do think that there destiny is a factor, considering that the Losties seemed to travel to significant time periods; considering how old the island probably is (it's gotta be old, come on), I don't think it's likely that they would flash to the time of Jughead, Rousseau's science team, Aaron's birth, and the time of Dharma at random. (Which reminds me, we still don't know who was in the outrigger that was shooting at the Losties, hmm..)
Anything Related to Jacob/MIB - Supernatural/Destiny
- This one is a bit of a no brainer, considering that smoke monsters, surviving knives to the chest, immortal Spaniards, and bottles of wine are obviously supernatural. I included Destiny because all of the stuff we've assumed to be caused by fate ('Everything happens for a reason') may have been Jacob's doing.
Walt - Supernatural
- This is just a hunch, considering that we probably will never see him again, and all we apparently know is that the Other's think he's important, he learns fast, and he causes birds to fly into windows. Oh, plus the creepy manifestations ("You've got work to do, John.") and apparent visions ("Don't open up that thing, Mr. Locke.")
Supply Drop - Scientific
- Remember in season 2, when Jack and Kate find a pile of fresh Dharma food in the middle of the jungle? Yeah, it still bugs me that we don't know how it got there when Dharma ended over a decade ago. My hypothesis is that either it was dropped there without the knowledge of the fate of Dharma, or that, like Daniel's experiment with the payload, there was a space in time between the island and the real world, and that the supply drop was supposed to land on the island years ago.
Desmond's Flashes - Scientific/Destiny
- Considering that they were caused by scientific means (electromagnetism), I'd argue that there is a scientific explanation for Desmond's flashes, as opposed to a gift given to him by Jacob or MIB. I don't think we've seen the end of his flashes, considering that they are a part of (in my opinion) the seemingly biggest plot hole thus far: if Charlie drowned to get Claire and Aaron rescued on a helicopter, why haven't they yet?
The Departure and Return of the Oceanic 6 - Destiny (and possibly Supernatural)
- Jack claims in the Season 5 finale that coming back to 1977 and blow up the hydrogen bomb is their destiny, and I have to agree. Whether that includes the significance of the flash-sideways timeline, their roles as candidates, or MIB's plan, is up to anybody. The only reason I'd suggest that it could be influenced by the supernatural is that perhaps somehow Jacob had a part in bringing them back to the island, through Ms. Hawking/Widmore/Ben, or that MIB gave them a nudge (via Christian in the Frozen Donkey Chamber, via 'Jeremy Bentham')
Miles' Ability - Scientific
- Unless this was a gift given to him by Jacob, I'd argue that Miles' power falls under the 'science-fiction' category. Up until the Season 5 finale, I assumed that Miles' gained his power through the Incident, much like how Desmond gained his from the Discharge. However, we still don't know how he got his power, so we can't be positive if it was or wasn't the work of destiny or supernatural powers.
Hurley's Ability - Supernatural
- Unlike Miles' power, I think that Hurley's ability stems from supernatural causes. There isn't any scientific rationality for talking to the dead souls of friends (but then again, when was there ever rationality in time travel, healing islands, and Ajira Airways' lack of observation of the Oceanic 6 all on one plane). Though there isn't any proof that Hurley got his gift from Jacob, I'd argue that it is in fact true.
Cabin Fever - Scientific
- Was it ever part of Jacob's or MIB's plan to have crewmembers jumping off boats wearing chains? I doubt it, so this falls under the 'Island's scientific, electromagnetic anomalies' category.
Charlotte Malkin - Destiny
- Yeah, that's right: the girl who drowned, they came back to life, and brought Eko to Sidney. This could be either scientific or supernatural, but does it really matter that much? The only thing that jumps out at me is that in the autopsy tape when she wakes up, if you listen closely you can hear her scream John Locke (I'm dead serious, no pun intended), and then she delivers a message to Eko from Yemi. I'm not sure if that falls under the Jacob/MIB umbrella, but to me that definately falls into the Destiny category. Unlike her father, the fraud.
Dreams and Visions - Supernatural
- On or off the island, I think that every vision we've seen is a manifestation of Jacob or MIB, trying to manipulate a character for their own means (with the exception of the mysterious boy who tells Fake Locke what he can't do, who is that kid?) You'd be hard-pressed to convince me otherwise without substantial proof.
Flashsideways Timeline- Destiny (with a hint of Supernatural and Scientific)
- This is the big one, the alternate timeline which you either hate, or hope that you won't hate later on. It's hard to comprehend the differenes between the original timeline and flashsideways timeline: how does blowing up a bomb directly or indirectly cause the island to sink, Sun and Jin's secret affair, Sawyer to become a cop, or Jack to have a son (if indeed it was the bomb that caused the secondary timeline to appear)? I'd argue (and this is my general opinion, based on general assumptions) that this is the destiny Jack was referring to, and that this is a world without the influence of the island, Jacob, or MIB (so actually, this would fall under the 'Destiny, caused by Scientific means, with a lack of Supernatural powers').
So there you have it. Feel free to comment, whether you agree or disagree with the labellings given. Trying to decipher science from supernatural will perhaps give us a bit of insight in what's coming up. The time-travelling season 5 was obviously scientific, but led us into the supernatural season 6, which is all about Jacob vs. MIB. Have we seen the end of Desmond's flashes? Is there a supernatural flair to the flashsideways timeline? And will the Hurley Bird make a final appearance? Only time will tell, we can only geuss if the explanations we're about to be given are in line with what we've assumed up until now.