I've already admitted how easily I suspended disbelief, and was shaken by the film's impact. Yet I cannot argue with the really smart catalogue of plot holes in this thread. Everyone here has raised good points.
SPOILERS GALORE: The most potent one, perhaps, is about the timing -- why stick this apparatus under the ground and wait until ... now? My theory, tied to something not much discussed, concerns the obvious parasitic nature of the aliens. Did they wait until the earth was so densely populated that they could feed off of the animal life (us!) so freely? I was startled by the squence when it was realed how they need to drain us for those blood-soaked-plants (right?) Was that a key component? They didn't just want to exterminate, or the death rate might've been more efficacious (as someone pointed out--it worked about as well as death rays did in FLASH GORDON, 75 years ago-zap this guy, zap that one, hundreds flee around them...).
I thought about how I enjoyed the over-the-top INDEPENDENCE DAY, but the holes were outrageous there AS they appeared. Remember the act three of that film, when Jeff Goldblum got into their computers? I remember turning to someone and saying "The aliens use WINDOWS 95!" All he had to do is connect via his modem (the technology is already quaint in 2005.) It always cracks me up -- going back to the 50s scifi -- how aliens are always 'advanced' in terms of technology, but somehow interface with ours when it's necessary to serve the story.
I also wondered why these alients, so hellbent on death, would bother to stick that compledx snake apparatus into one farmhouse basement. Why spend all the time there? Why not go ... say ... to NASA, or more survival-oriented, to a blood supply? They were sometimes suddenly fascinated with a handful of individuals, after being seemingly oblivious. I didn't get that. But it did make for very intimate scenes, which these movies despearately need.
Anyway, this thread proves that this movie does not have fewer holes than any other. But for me, because Spielberg created a gripping sense of dread and a real threat, and maybe because he employed 9/11 as a metaphor, I just found myself willing to suspend disbelief at every turn. It was dark, grim, and frightening. At least until I got home.
"I'm a comedian, but in my spare time, things bother me." Garry Shandling