So here's the things I'd like to know. Some of these will likely be answered in Season 6 but most probably won't unless Damon and Carlton publish some compendium of LOST trivia after the show ends. Nevertheless, as I rewatch the entire series to date over this hiatus, I'm going to collect these questions. After the series ends, we'll see where we stand.
1. Are Amelia and Amy the same person?
2. How did Ethan become an Other?
3. Where did Karl come from?
4. Why couldn't Desmond sail out of the influence of the Island?
5. What happened to the Elizabeth?
6. Why the Viking funeral for Colleen?
7. What force (good/bad/Jacob/Smokey/etc) was manipulating Locke's dreams and Smoke Lodge visions and also keeping him from walking and talking?
8. What was the Pearl's original purpose since it seems to predate the Swan and the Incident at the Swan?
9. Was Jacob communicating with Ben as Leader of the Others and if so, how?
10. How many polar bears were there?
11. Was Tom part of the original DI? Of Widmore's Others?
12. What is the deal with the Island pregnancy problem? When did it start?
13. Why did Mittelos go after Juliet? What is Ben's obsession with her including an explanation of the painting?
14. Who created the Room 23 video and to what end exactly? Who has undergone it's application?
15. Flashes Before Your Eyes established the existence of a time loop. When does it start and end and who is aware of reliving it? Does Ellie's statement to Penny at the hospital establish that the loop has ended once 316 returns to the Island?
16. Why mark Juliet in a place no one can see?
17. Cindy and the kids and the other Tailies taken -- what's the deal?
18. When did the Purge occur?
19. Why exactly do the Others have such a superiority complex like Mikhail when talking to Kate and Pickett's attitude to Sawyer?
20. Are things like Kate's horse and the cat named Nadia on the Island because of Jacob? The Man in Black? Are these coincidental occurrences how Jacob and MIB interact with the "players" on the Island?
21. When and how did Carol Littleton's coma end? (I hope it was Jacob.)
22. What the heck makes the Others (like Mikhail) have such faith in their magnificent leader (presumably Jacob) despite never having seen him?
23. How did Tom get off and back on Island post-purpling? And was he the one who brought Cooper to the Island? If not, who did and when?
24. What's the story behind the blond woman with the guinea pig painting in Ben's house.
25. Were Desmond's visions during his flashing period true or lies, especially the flashes when Naomi lied given that he saw both Charlie die and Charlie holding the parachute?
26. Why do Locke's legs stop working at times on the Island?
27. Who told Ben to have the Others build a runway?
28. Who/what was Taller Ghost Walt?
29. Who besides Christian Shephard was in the cabin when Hurley saw it in episode 4.1, and why did the cabin move?
30. What is the deal with the changing photo frames in the house Miles first ghostbusts?
31. What is the deal with The Whispers?
32. What caused the horse to intervene in Kate's escape and why is the same horse on the Island?
33. Was Kate hallucinating or did something inhabit Sawyer to make him seem like Wayne?
34. Did Ben get caught in Rousseau's trap on purpose? If not, where was he going?
35. What is the deal with the injections -- those given to Claire; those in the Swan?
36. Why did the Others want Aaron, but not Claire?
37. How do the food drops at the Swan work?
38. How do the people that Ben had Sayid execute, like Peter Avellino fit into the story? Same with Abaddon. How did he come to work for Widmore?
39. Why did Kelvin and possibly Radzinsky pull the whole quarantine charade in the Hatch?
40. How does Penny's encounter with Desmond at the LA track jive with their encounter in The Constant?