There are some real complexities here, because some areas are approached differently, like entrance courtyards becoming clock tower courtyards, etc, and maybe one day I will use books and websites to try to clarify these points. But, let's start off with some clear changes:
Prisoner of Azkaban changes:
During the first two films, Hogwarts as a whole was decidedly flat. Hagrid's was reached by walking out the front door and across a flat field.
Compare to the change in Prisoner of Azkaban:
For Prisoner of Azkaban, the setting was altered dramatically to reflect Hogwarts' position in the Scottish mountains. The covered bridge was seen for the first time. We saw the stone circle overlooking Hagrid's hut, which was now much further from the castle.
The front door was reached via a courtyard rather than opening straight onto the lawn. Other changes include new towers here and there as well as the style of pre-existing towers being changed.
Goblet of Fire changes:
Goblet of Fire featured more of the castle itself as a whole as Harry and the dragon flew and climbed all around it. It confirmed that the changes in PoA were there to stay. Goblet of Fire is the first time we see the Owlery, a tower far from the rest of the Castle where the delivery owls are kept.
Order of the Phoenix changes:
There were changes in the overall layout for Order of the Phoenix which are more subtle, but the clock tower was seen more prominently and in a new position.
Half Blood Prince changes:
Half Blood Prince saw the introduction of the Astronomy Tower.
Deathly Hallows changes:
Looking at Deathly Hallows as one instalment, a stone bridge of sorts was added to the entrance mostly for a more dramatic siege. It appears to be that they moved the original viaduct from going across the front of the castle from left (near the entrance) to right so that it was projecting away from the entrance.
If you are interested in significant interiors, the staircases were changed dramatically.
Traditionally the stair cases looked like this:
In this film, Harry fights Voldemort on stairs which look like this:
(People debate that they are different stair cases, but I have chosen this second image as it shows that this large, straight group of stairs is just beyond the Entrance Hall, where it was not before.)
While the entrance courtyard changes frequently in the films, it certainly is much larger in Deathly Hallows Part 2:
This is from The order of the Phoenix - it looks large, but compare the number of gargoyles.