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.
Ogilvy mentions that the Japanese figured out how to kill the aliens first. Japanese culture is known for the tactics Ray eventually uses.
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." Ogilvy is a threat to Rachel's life, and therefore something she would need to worry about. By killing him, Ray is effectively taking Rachel's "worries away."
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?
One has to imagine that Rachel is going to need a lot of therapy after everything she's been through.