Why does the Martian's weapon leave clothing intact? Its an highly-focused enhanced radiation weapon similar to a Neutron Bomb, which is designed to wipe out enemies soldiers but leave their infrastructure relatively intact. This is why it dessicates humans into ash but less of an effect on clothing (and armour). Similarly, it also demonstrates similarlities to a neutron bomb's having some concussive force, in the way that it impacts objects. It isn't a "heat ray" at all, as throughout the films, we never see it ignite objects, the only fires seen are clearly caused by explosions from other sources.
When the aliens go through Ogilvy's basement, they all look at a picture of what's presumed to be Ogilvy's deceased daughter. Notice that they all look at it the wrong way (as in, never viewing it upright). Common from something that's never seen a photograph before.
The aliens somehow get gigantic war-vehicles to come out of the ground. See the Headscratcher page for more in-depth discussion.
The plants that the Martians are growing are a vein like substance. If you wonder why they chose this design was because one of the writers Percival Lowell who used an observatory to research mars and its "canals." However, these canals were actually the veins inside his eyeballs.
When Rachel sings her lullaby as Ray goes to kill Ogilvy, we see Ray walk into Ogilvy's room and slam the door shut as Rachel sings the line, "waiting to sail your worries away." Ray kills him because he's a threat to Rachel's safety- something she would need to worry about.
When the Tripods first emerge from hibernation, their whole modus operandi appears to be mass slaughter. They kill everything that moves, level entire neighborhoods, and just generally seem bent on the total extermination of humanity. After a few days, though, they seem to change their approach completely. It becomes clear that they want to capture human beings alive, because they need blood to fertilize their "crops", and humans just so happen to be (by far) the most widespread large animals in the area. While these two strategies seem to conflict at first glance, on closer consideration, they fit together disturbingly well. Between the initial attacks centered on major urban areas, the fact that the Tripods make their presence known very clearly with a sound that people would quickly learn to associate with sheer animalistic terror, and the way they fan out into the countryside in pursuit of refugees, it's pretty obvious what they're doing. They're flushing people out into the open, where they'll be trapped either on foot or in massive traffic jams, making them easier to pick off one by one. The massive flood of survivors also functions to make military logistics a nightmare and, with the Tripods always near large crowds of humans, the nuclear option is pretty much off the table. While megaton-range explosives would probably be enough to break through a Tripod's shield, the use of enough to make any meaningful dent in their overall numbers would likely kill too many people to be worth the trade-off.
Just before the first lightning storm hits, Ray is watching the growing clouds from his backyard and has a brief exchange with his neighbor, who is carrying her toddler. The scared mother and child go back into their house - this and all the other nearby houses are later destroyed when the Martian war-machine destroys an elevated freeway. Were they able to escape beforehand?
The plane that crashes into the cul-de-sac was likely in the air when the aliens attacked. It was flying into Boston and preparing to land with everyone on board completely unaware of the horrors occurring on the ground, except for the pilots who were befuddled by how air traffic control suddenly went completely dark. In a scenario similar to Die Hard 2, with no clearance for landing the plane simply circled around overhead for hours while the pilot tried repeatedly in vain to engage with air traffic control until it ran out of fuel and crash landed. The plane being out of fuel also explains why it didn't explode into a fireball on impact, thus allowing the passengers on board a chance at survival as long as they were properly braced - not to mention that the blast would have killed the protagonists as well. Then consider that all the air traffic in the areas that aliens attacked likely met similar fates - they crash landed into random areas with zero guidance from air traffic control after exhausting their fuel reserves.
One has to imagine that Rachel is going to need a lot of therapy after everything she's been through.
Rachel's line "Is it the terrorists?" implies that 9/11 happened in this film's universe, making this the second traumatic event she's experienced in her childhood.
We see the Tripods spraying blood all over everything to seed the Red Weed. Horrifying enough on its own, but just how many people did they have to kill in order to pull that off? An average adult human has a little over a gallon of blood, assuming that they can drain people so efficiently that there's almost nothing left behind. To use it that effectively as fertilizer, they had to be running through tens of thousands of people every day.
The utterly banal behavior of the alien soldiers when they leave their ship and explore the house the humans are hiding in. Like the soldiers in "Schindler's List" talking about the piano player playing Bach, they don't come across as some incomprehensibly alien creatures, but just very ordinary scummy soldiers convinced that the people they are killing have no right to live. Evil truly is banal.
