In the cinema, with the sound system going full-bore, the initial tripod appearance scene nearly gave me a heart attack - not out of fright, because I knew full well what was going to happen... but it was just so... visceral. I was really buying into it, and when the tripod sounded it's horn for the first time, I grinned like a maniac, thinking, "Oh, man - perfect.". Another little moment that I love that I never hear mentioned is when Ray is sitting under his kitchen table in shock, and his daughter touches his shoulder. The flinch is just great.
The highway scene is also great. I didn't even cotton on to the fact that it was a single take. It's just a good, frantic scene - even with the bullshit psychology trick. I feel Cruise really sells Ray's nearness to just cracking up at that point. The car/crowd scene later on is one of the more upsetting film sequences I can recall, and nary a tripod or alien in sight. That guy clawing his way through the windshield is just so... zombie.
Tim Robbins? Well, at least we know what we're getting into with him from the first shot. I start chuckling now when I see him holding up the lantern to his face... "Hi, I'm not crazy!". I would have been fine with not seeing the aliens until the end.
Maybe the basement sequence feels longer than it is because the final act seems rushed.
The grenade? It bothers me just a little, I suppose. Perhaps if the soldier could have done the actual deed, with Ray being the one who pulls him back down. Ray would still get to be a bit of a hero (and it'd be a sort of a callback to when he lets Robbie go), and the end result would be the same. When I see this sequence now, I mostly think of Spielberg talking about how unpleasant it was to shoot.
I think I could stomach the ending better if the family had been just slightly more roughed up. Personally, I'd have been in bunker mode at that point, not cardigan mode.