I will update this section as new theories are introduced and old theories are solved/or found to have nothing to them. I apologize in advance beacuse it is kind of long. Each theory has a heading in italics to help you navigate through this post.
Remember, these are just theories:
~DJ Dan and Peter Thompson either know each other, or are the same person. We know that one of the cities DJ Dan could have been born in is Terre Haute, In...that's where Peter was born. We also know that DJ Dan was born around 1960. Peter's year of birth is 1959. Original theory posted by pwyll at thelostexperienceclues.com.
~Walt connected to Retrievers of Truth website. On the ROT website under the “History and Notoriety” tab there is a story attributed to the date 1899 about a yellow lab born to a black lab mother in Australia. The interesting thing about the story is the names of those involved. Check it out: It all takes place in Australia. The dog was owned by the Porter family. The yellow lab puppy was rescued by a child of a servant named Lloyd. The story included in a time line created by a Vincent “Wally” Bole. Now the Walt Connection: Walt’s mother was named Susan Lloyd. She left Michael and married her boss Brian Porter. They end up living in Australia. When Michael and Walt left to return to LA, Brian Porter gave Walt Lloyd a yellow lab named Vincent. Original theory posted by Xb4all at thetailsection.com.
~What happened to Alvar Hanso, and who is running THF now? Here's what I think: 1. Alvar Hanso was the only person at the Hanso Foundation who has/had access to the Valenzetti Equation. 2. He used this knowledge to direct the Foundation's activities, but never let anyone know exactly and completely what the equation consists of. 3. Alvar Hanso disappears, taking the Valenzetti Equation with him. Obviously, he disappears after the Madrid Incident. Why? We don't know if he ran into hiding or if he was captured or killed. 4. Mittelwerk and the others left at the Hanso Foundation use the VIK Institute and the autistic savants to re-create the Valenzetti Equation, using what little they already know about it. Obviously there is conflict between Mittelwerk and Hanso, but we don't know if that's what drove him away: Mittelwerk took over and then- imprisoned, killed, etc. Hanso- caused him to go into hiding. OR, Alvar Hanso ran away, was killed, etc., and then Mittelwerk took over. Original theory posted by Matt the Pale on the research disscussion blog.
~Hugh on Jimmy Kimmel...the real Hugh? The whole Hugh Mcintyre thing on Jimmy Kimmel. We're not sure if that's the real Hugh. Maybe the real Hugh went missing with Hanso and this new guy is taking over for him as Mittelwerk is taking over for Hanso. Only not to cause a panic, he assumes Hugh's identity, and tells people Hanso's fine. Original theory posted by damn the man on the research discussion blog.
~Hanso and alchemy. It's possible that the Hanso Foundation and Alvar Hanso are somehow related to alchemy. Alvar Hanso is an arms dealer, which means he sells weapons for money. Figuratively speaking, this means he convers lead (guns) into gold (money). But on a more serious note, someone over at LostPedia made the connection between Magnus Hanso and St. Nicholas the Great. Read it for yourself here, but remember it has spoilers! Also, the Hanso Foundation is trying to extend lifespans and eradicate disease -- the same things that the alchemists were trying to do with things like the panacea and the elixir of life. We've already seen several connections in TLE to the alchemists. For example, the "Japanese Mouse" that the people over at RoT talk about -- that mouse is Kaguya, the parthenogenical mouse, but in the Japanese legend, Kaguya the moon princess gave the Emperor of Japan the elixir of life. Original theory posted by Matt the Pale on the research discussion blog.
~The DHARMA LOGO and Bagua. The Swan logo is an example of the use of the Bagua concept, as either a type of navigation [compass], or fengshui. The blast door map is the octogonal shape. It's possible that the Bagua symbols could match up with the island, and possibly to the hatches. These are some of the possibilities: This is by just putting the Bagua symbol right over the blast door map of the island as is with no moving. This is by setting "Fame/Rank" over the Flame hatch because of the fire reference. And this is damn the man trying to set "Family/Health" to where the "foot" is because "Family/Health" has a reference to a foot in it. And the way it's set up, "Fame/Rank" lies near the Arrow which had the glass eye, and "Fame/Rank" has references to an eye in it. Original theory posted by TaiwanGuy in the IRC. Pictures by damn the man.
~Dr. "Wally" is Alvar Hanso. Here is a comparitive of the doc with the hidden picture of A.H. at thf.org Original theory posted at Lostpedia.com.
~The Electromagnetic Research Initiative. It may possibly have a direct correlation to the huge magnetic force that was contained by punching in the numbers every 108 minutes on the show Lost. Original theory posted at Lostpedia.com.
~The Life Extension Project. Some of the DHARMA/Hanso people seem to change over time (Candle uses differant name and no longer has bad arm), the clues have shown signatures to change over time, and in McIntyre's interview with Jimmy Kimmel they discussed how he didn't look like his picture; it may be that the life extension project involves some kind of "body/mind swapping" technique where people migrate their minds into younger bodies as they grow old. Alvar Hanso may be a recluse because he inhabits a body which is too young to miss. Original theory posted at Lostpedia.com.
~Liddy is Ms. Klugh. Liddy Wales character could be Ms. Klugh from Lost episode "Three Minutes." Who seems to be a major figure in the others and therefore probably DHARMA who are obviously connected to Hanso. Original theory posted at Lostpedia.com.
~Time future theory. The ARG is possibly set in a future time to our reality. We see this in multiple time discrepencies in the game. For example, the RoT board having posts "in the future", and SPEAKER's comment about the series being representative of past events. It is possible that the show "Lost" is set in the past, we (meaning those of us playing the game) are set in the present, and the game is set in the future. Original theory posted by 007surge and damn the man on the research discussion blog.
Persephone is Rachel who is also related to Alvar Hanso (possibly his daughter/granddaughter). 1. P.'s goal does not seem to be to take down Alvar Hanso as much as to locate him. "Where is Alvar Hanso??" has been prominent in a huge number of her hacks. 2. Mittlewerk's apparent recognition of Rachel. Maybe he knew her as a child and, thus, recognized her but couldn't place her face. 3. The overall prevelence of parent-child relationships in the show: Jack, Locke, Michael/Walt, Sun, Anna-Lucia, etc. 4. "Let the force be with you."- Perhaps the most prominent disfunctional father-child relationship in movie history. Could Rachel have been hinting at her true identity? Original theory posted by taiwonguy via email to the research team.