Question: What happened to Ogilvy?
Answer: Ray couldn't trust Ogilvy to be quiet when the aliens arrived. So Ray had to kill Oglivy in order to save him and his daughter.
Question: Is it realistic to think that Manny, the garage mechanic would have NO idea of what was going on when Ray steals the van from him? After all this is probably about 20 minutes after the Tripod emerged a few blocks away. Surely news would travel faster than that! And you'd think Manny would have felt the massive tripod moving or heard the destruction.
Answer: There's no electricity, so the only way Manny could have heard was through word of mouth. The few survivors from the initial attack scattered in different directions and if any happened Manny's way, they were probably too busy running to stop to explain anything to a garage mechanic. As for his awareness of the destruction, anything he may have felt or heard he likely dismissed as further manifestations of the freak electrical storm.
Question: Does anyone have any clue as to why the aliens are vapourising people when they first appear? They never seem to do it again after that one scene (instead opting to grab them and drain them). Any help would be appreciated.
Answer: The aliens saw the humans as an immediate threat to their ship getting out from underground, so opted to vaporise anyone in the near vicinity so that it could leave the ground unimpeded.
Question: When all of the people are trying to get on the boat, how does a tripod just randomly come out of the water like that?
Answer: While it's never explained, there are several possibilities: as all the tripods were buried deep underground, this one may have been lodged below the lake and was just emerging. Also, a tripod could have "walked" from somewhere else, then went underwater to explore, and, attracted by the ferry's noise and movement, surfaced to investigate. It's also conceivable that, observing how ferries worked, it slipped underwater from further away and ambushed the boat, or the tripod was simply making a crossing from one shore to the other (traveling underwater if it was deep enough) and just happened upon the ferry when it did.
Question: Is there any indication as to where the aliens come from and what exactly they want?
Answer: In the original George Pal version they were Martians and the reasoning for what they were doing was never explained. In this version, its never explained where they come from, but their mission is simple, to eradicate human life from Earth, and use our bodies to fertilise the planet, probably so that they can colonise the planet for themselves.
Question: Several other answers and corrections state that the reddish liquid sprayed by the tripods was what essentially grew the red vines. However I thought I heard someone in the film say something along the lines of "using us (i.e. blood) as fertiliser". Can someone please clarify?
Answer: Since the tripods tended to spray the red fluid shortly after pulling a human into themselves, it seems a good assumption that the red fluid is essentially blood. Given this, it seems likely that the "spore" of the vines is spread in the red fluid.
Question: In the scene where Tom Cruise and co. are in the tripod's 'basket', a man is sucked up into the tripod and no-one does anything, but as soon as its Cruise's turn everyone grabs him to try and help, why?
Answer: As there is no audio commentaries its hard to know for sure why this is, but when the guy is sucked up the people in the basket are trying to get out and most are panicked. Add to that they weren't sure what was going to happen to the guy might have made them unsure of helping him out. The next time they would know what was going to happen and perhaps were now prepared to help.
Question: At the end, a tripod collapses after behaving erratically for an hour, because the aliens inside were dead or dying. If so, wouldn't the tripod just stop moving and stand there because the aliens were too sick to operate it?
Answer: Depends on exactly how the disease affected the aliens. They might have entered a state of dementia and started piloting erratically, or even just have muscle spasms that knocked the controls around inside the cockpit.