Nice thread there.
Much of what I would comment has already been said, but here are a few more or less random things from me.
I think that one of the worst changes was the omission of the "Conspiracy unmasked" part. They wouldn't necessarily have to do the entire Crickhollow side plot, but had they only filmed the most basic essentials of it in a few minutes, it would have given Merry and Pippin a lot more depth - not to mention a more decent introduction.
I think the scenes in Bree are the only ones where Mortensen is really a good fit for Aragorn. I keep thinking that PJ had this introduction more in mind than the later story when he casted him. Mortensen makes a good Strider, but not a good Elessar.
The ranger sword has been mentioned - note that Strider is also given bow and arrow in the movie. I think this was a good deviation.
One change I liked was the introduction of Elvish lines. I know that half of the words and grammar was probably made up, but the sound was at one level with Tolkien's own. When used in conversation it sometimes seems a little forced, but I really liked it in the scenes with Arwen at the Ford of Bruinen and Saruman at the top of Orthanc conjuring the wrath of Caradhras (whether those scenes themselves were good or made sense is another thing). It's a pity that many original Elvish lines were omitted. It's no surprise
Namarie didn't make the cut, but a little
A Elbereth and a glimpse of the Hall of Fire would have been nice.
The Breaking of the Fellowship - the way it's been done is ok, but here it could really have been better had they stuck to the original text more. The dialogue between Frodo and Boromir is one of the best of the entire LotR. They surely could have saved a few minutes of screen time for it.