Jeremy Brett as Sherlock Holmes. 'Course, all we have are some 100-year-old drawings to go on.
Matthew Broderick (video clip) as Colonel Robert Gould Shaw (scroll down; right side)
Jason Harner as Gordon Stewart Northcutt in Changeling.
William Devane as John F. Kennedy in The Missiles of October. Critics agreed that he absolutely nailed that role. He was nominated for an Emmy.
Martin Sheen as Bobby Kennedy was also excellent. Sheen later played JFK in a TV movie, but Devane was a hard act to follow.
HBO ran a movie called “The Rat Pack” in 1998. Joe Mantegna was uncanny as Dean Martin. Don Cheadle was also impressive as Sammy Davis, Jr.
Another mention for Josh Brolin, but this time as SF Supervisor Dan White in Milk
Just to be timely, I thought the actors they got for Rorschach, NiteOwl II, Comedian, and Silk Spectre II were spot on appearance wise in Watchmen, and all but SS were spot on acting wise as well. Manhattan was a CGI puppet so it’s hard to tell with him. Ozy was tragically miscast and misclothed…
I almost posted the Cheadle thing! Mantegna was also a good fit. And your other picks are winners, too. We seem to see people’s looks a lot alike.
Another I almost posted was Sherilyn Fenn as Elizabeth Taylor, but I chickened out. 
Pictures of Charles Starkweather are not as close to Martin Sheen as I had remembered when Badlands was new, but I have always thought that Sheen tried his hardest to channel James Dean, too.
While fictional, I’ll say that Alec Baldwin was perfect as Jack Ryan. After reading the first Clancy books, my mental picture of the character was almost exactly matched by Baldwin, both physically and his performance.
Alas, whatever his merits, Harrison Ford never quite felt right as Ryan, not even an “older” Ryan. And Willem Dafoe may be awesome, but he’s NOT John Clark.
(Actually, I thought Liev Schreiber made a great Clark in “The Sum of All Fears”-- too bad the movie bastardized the story, and while I’m not as hard on some people hit on Ben Affleck, it was still such a weak deal all around).
Physically (and spiritually), Scott was a fantastic choice.
Thankfully, however, Scott’s unforgettable voice was MUCH better than the high-pitch of Patton’s real voice (here’s a link to a sound file of Patton speaking).
BTW, I’ve heard that the real Abraham Lincoln suffered the same deal-- contrary to many actor’s performances, in real life he apparently had a high voice.
I haven’t seen the movie but I would guess that Fred Thompson was a perfect match for Fred Thompson in the movie Marie.
Ed Harris as John Glenn (The Right Stuff).
Ed Harris as Gene Kranz (Apollo 13).
What? I didn’t realize there was anyone besides Jessica Alba as Nancy the stripper in that movie. 
John Malkovich was uncanny as John Malkovich in Being John Malkovich.
I thought Christopher Reeve was a good match for both Superman and Clark Kent.
Richard Belzer as John Munch. Read the book HOMICIDE was based on, it’s hard to imagine anybody else in the role.
As a big Clancy fan, I agree that though I like Harrison Ford, I never thought he was as good a fit for Ryan as Baldwin. I wish Baldwin would have kept with the franchise.
And I also agree that though Willem Dafoe is great, he was not my picture of Clark. I always thought Howie Long (former Raider, now sportscaster) would have been the perfect Clark (if he could act).
But while we’re on the subject of “Clear and Present Danger”, I did think that Raymond Cruz was the PERFECT Chavez ("'ding"). And it was fun to see him “in the flesh”.
If we’re going there, Julia Roberts was brilliantly cast as a regular woman who happens to look enough like Julie Roberts to impersonate her in a wacky scheme in Ocean’s 12.
Dan Hedaya as Dick (Nixon)
Madonna as Eva Peron
Melissa Gilbert as Laura Ingalls Wilder.
Vivien Leigh as Scarlett O’Hara. I’m re-reading Gone With The Wind, and the descriptions of Scarlett sound like they were written for Leigh.