OK, me first !
I'll start with the picks I disagree with:
Jackie Brown: good film, yes. Best of the 90's???!!! C'mon. I know the 90's weren't the best but there has to be a better choise than this. Much too self-conscious in its writing style. the acting is the element which raises this movie above "annoying" status to me. They are all fun to watch. But "best"?... nope.
Fear and Loathing: Firstly, I must say I am a Gilliam fan. Love his work. And even though this movie has some of his signature visuals and unique story-telling qualities I love from him, it is just not a good movie. Period. Again, the actors are having fun and doing a good job, but I think Gilliam needed to take a page out of Cronenburg's book when filming his kind of material... less literal... To me it was just a mess of ideas going nowhere.
Existnz: OK, I put it on my "don't agree" list, but I can't come up with a real reason why. It was good, following ideas cronenburg has toyed with before, and in some cases, better than the Matrix, but to me it just felt like a film that needed more time --- or money --- or something.
OK, I admit it, I can't come up with a good reason why tis isn't one of the "best"...
Three Kings: Good movie, again. But not "best". I agree with Cail here, but with less of his vehemence

It's kinda fluffy for me.
Grosse Point Blank: This film always gets talked about. And to be honest, I have not frik'n idea why! It is average on all accounts. Boring almost, except for an amusing shoot-out scene in the house with Cusak and Akroyd...
Braveheart: One of my picks for one of the most overrated movies ever. Rob Roy was far better... ('nuff said)
The Fugitive: ????

my god, this was a slightly above average thriller-type movie. Pop movie, but not "best". (sheesh)
Pretty Woman:
Now my "AGREE" list is much longer (I will merely quote most names):
Eyes Wide Shut: Say what you will about this, the movie is beautiful, haunting and deep. Almost every scene is engrained in my memory.
Dark City: Except for the little voice over prologue to this movie, it is perfect. I am glad to see someone giving it its due.
Hudsucker Proxy: There is a part of me that is surprised this movie did not do better. It is funny, charming and poetic. And the performances are delightfully over-the-top.
Ronin: Ahhhhh, a fantastically tight movie that brings back the glory days of this type of thriller.... Two of the best car chase sequences ever put on film...
Glengarry Glen Ross: We know the script is great, but MAN when you have a cast like that!!!! AMAZING!!!!!!
Zero Effect: a quiet, clever and sublimly funny film that totally flew under everyones radar. (hmmm, maybe not "best" but definately worth a look or two)
LA Confidential: great film making on all levels...
Barton Fink: It took me no less than 3 viewings to realize how great this 'difficult' film is.
Miller's Crossing: Tnak god someone put this on their list! In my humble opinion it is actually better than Goodfellas.
Matrix: this one HAS to be on the list because of it's thought provoking script, mind-bending notions, FX and action sequences.
Being John Malkovich: Truly original in all ways!
Se7en: the movie that spawned a thousand copies in idea and style...
Usual Suspects: Great!
Out of Sight: This is a fantastic bit of film making. There are so many elements to the script that make it wonderful to watch over and over again. And we gwet a good performance from Jlo. The directing and editing are amazing (a nod to The Limey in that respect, which I am disappointed did not make the list).