Addressing your various points:
1985: I maintain that Witness is a better film than Out of Africa, The Color Purple, etc. Although Ran is one hell of a movie, and I'd have accepted that as a Best Picture win too. I'd also have accepted a win for Back to the Future (though obviously that was never going to happen).
1989: I would have accepted any of the following for Best Picture over Driving Miss Daisy: Field of Dreams, Born on the Fourth of July, Glory, My Left Foot, and obviously Do the Right Thing. But in truth, I prefer Dead Poets Society to all of them. Tom Schulman wrote the screenplay, by the way.
1998: On the Day of Judgement, someone will have to answer to God for The Truman Show not getting a Best Picture nomination. It should have won. I've made the detailed argument many times, and stand by it, including elsewhere in the comments, as at least one person mentioned the Saving Private Ryan thing. Much as I think Saving Private Ryan is a great and influential film, The Truman Show is a better film overall (again, I got into why elsewhere in the comments). I also love The Thin Red Line, but The Truman Show should have won Best Picture (with Spielberg winning Best Director, which he did).
2003: Here I agree, he didn't stand a chance, which is a shame, as I think he would have won in any other year. I don't begrudge Peter Jackson his win, as The Lord of the Rings is a monumental achievement.
Agreed re: Altman and Lumet never winning. Absurd. :)