title says it all... the Matrix Reloaded, with the oracle comes to mind

Michael Gambon in Harry Potter and the Chamber of Secrets. Playing Dumbledore after the death of Richard Harris.

The Dark Knight Rises

This doesn't happen a lot due to the fact that most of the time, they find a way to write the character in question out of the story. Harry Potter was an exception, since those stories were already set in stone.

The actor who played Don Tommasino (the Don who takes Michael in when he's hiding out in Sicily) in The Godfather died so they replaced him for The Godfather Part III.

Toy Story 3

Who?

Brandon Lee had talked about Crow sequels, though none of the follow ups were in the works at the time of his death.

That would be rewritten, not recast unless I am mistaken.

John Prosky replaced Richard Jordan in Gods and Generals, but I don't even remember if his scene(s) made it into the film.

EDIT-Remembered another, George C. Scott replacing Lee J. Cobb in Exorcist III

Yup. This seems to happen more often for voice-acting (I'm guessing Tom was thinking of Jim Varney)

Others:
Homeward Bound II (Ralph Waite replacing Don Ameche)
The Hunchback of Notre Dame II (Jane Withers replacing Mary Wickes)

I won't even touch:
Bambi II
Jungle Book II
Lady and the Tramp II

you are correct.

Also with The Matrix movies, Aaliyah was recast by Gina Torres.

oh yeah...totally forgot about that recast

Exorcist II: The Heretic also had to undergo rewrites due to the death of Cobb.
He was to reprise his role as Detective Kinderman as one of the main characters and in a much bigger role than he had in the original.

I didn't even notice there was a different Oracle.

Really? That really stuck out to me because they didn't look or act anything like eachother.

Yep, you got it

All of the Brucesploitation pseudo-sequels come to mind, though they never would have been made if he hadn't died.

as a kid....I thought they were all Lee. I grew up thinking for a good while probably around till I was 15...that Lee made a shit ton of movies. I still like many of them...but...for sake of nostalgia.

I immediately noticed it but I had no idea the first oracle passed away

Yeah, that's the first one I thought of, too.

IIRC, the original plan was to have Eric be denied "heaven" because he went off-mission, and any Crow sequels would have had Eric Draven continuing his mission of vengeance against other wrong-doers.

Imaginarium of Dr. Parnassus

Pink is replacing Brittany Murphy as Gloria in Happy Feet 2.

Is that a sequel to something?

Plus it was written into the dialogue that she wasn't the same.