According to Aurora and Phoenix (ages 7 & 5) these are good from your list:
AGENT CODY BANKS
AGENT CODY BANKS 2: DESTINATION LONDON
BEETHOVEN (2nd and 3rdavailable)
CASPER
CATS AND DOGS
CHICKEN RUN
DR. SUESS' CAT IN THE HAT
HOOK
HARRY POTTER AND THE SORCERER'S STONE
HARRY POTTER AND THE CHAMBER OF SECRETS
HARRY POTTER AND THE PRISONER OF AZKABAN
THE IRON GIANT
JUMANJI
KANGAROO JACK
LEMONY SNICKET'S A SERIES OF UNFORTUNATE EVENTS
MADILINE
RACING STRIPES
RUGRATS IN PARIS: THE MOVIE
RUGRATS GO WILD
THE ROAD TO EL DORADO
SCOOBY DOO
SCOOBY DOO 2: MONSTER'S UNLEASHED
SHARK TALE
SHREK
SHREK 2
THE SPONGEBOB SQUAREPANTS MOVIE
SPY KIDS
SPY KIDS 2: ISLAND OF LOST DREAMS
SPY KIDS 3-D: GAME OVER
STUART LITTLE
WILLY WONKA AND THE CHOCOLATE FACTORY
THE WIZARD OF OZ
YU-GI-OH
I'm embarressed to say I've only seen a handful of the movies you list, myself. I do like Chicken Run enough that I would sit through it, the HP ones, the Shrek ones, The Wizard of Oz, and Willy Wonka... I've seen Iron Giant, Jumanji, and Spy Kids too many times to go see them again if they were shown for free in a park, but since I haven't seen the Lemony Snicket one, I would probably look forward to going to that... The 2nd and 3rd parts of Spy Kids aren't as good as the first one; HP only gets better w/each release- but each is a little more mature subject matter, a little darker a story... My kids were jumping up and down over just the titles of the Rugrats movies, but they make me gag, quite honestly.
Scooby Doo sucks A$$, but otoh, my boyfriend, who is a 51 year old physicist will sit and laugh his a$$ off through them w/the kids.
One that's not listed, but is better than Princess Monoke is "Spirited Away," THAT story is unusual and less well known, but holds interest for all ages, imnsho...