Tinker Tailor Soldier Spy - The recent film adaptation is so realistic that it almost feels heavy-handed about it. It's aggressively drab and un-glamorous, and it never attempts to lead the viewer by the hand. Result: confused viewers. Bonus realism: some of the things that author John Le Carre made up for the book were later adopted by British Intelligence.
Lord of the Rings - It's amazing that a fantasy world can be so completely realized on film. Especially a world in which wizards are prone to spouting exposition, and giant winged monsters can fall to their deaths.
The Island - Fun (if stolen) sci-fi flick that handles pretty well, right up until the point where clones learn Latin from their DNA. They hand-wave around it, but it's a major plot detail that doesn't quite scan.
Pi - I used to hate this movie, and yet everyone assumed I should love it because I'm was a math major. The problem is, this isn't a movie about math, it's about mysticism. My opinion has softened over the years, but some of the math assumptions--namely, that you can perfectly model complex systems using patterns (as opposed to regression)--still grate a little.
Transformers - Of all the ridiculous things in this movie, what bothers me the most is that the NSA has buildings with glass walls and is staffed with foreign nationals. Or anything John Turturro's character does. Or the way hacking is portrayed (is it ever portrayed well?). Actually, very little about this movie is believable except the giant robots that turn into cars and wreck cities. But since they got most of the screen time, I give it a pass.
Jurassic Park - Mixed bag here. Some of it is an artifact of its age--we now know that dinosaurs were feathered, and we didn't know that in 1993. Of course, we now also know that DNA has too short a half-life to be preserved for tens of millions of years. But dammit, even in 1993 we knew that velociraptors were only two feet tall.
Tomorrow Never Dies - Leaving aside the regular James Bond camp, the stealth boat is a pretty big problem for me. "Stealth materials" are plastic, boats don't have to evade radar, they have to evade sonar. On top of which, submarines already do that and do it better.
Braveheart - This was one of my favorite movies until I learned about how horribly wrong it gets the details of Wallace's life. There's the purely aesthetic--wearing blue woad, kilts worn centuries before they were adopted, changing Marion's name to Murron. Then there's the perplexing--re-writing all the battles to take place in open fields (Sterling was a bridge, Wallace did not invent chiltirons, and Bannockburn was a swamp). Then there's the downright insulting. Wallace could not have cuckolded Prince John, since he died six years before John was married. Add to all of that the homophobia and anti-Anglicism, and it's a very difficult movie for me to watch anymore. But the worst part is the opening line of the film, which chides people for questioning how accurate it is.
Roger & Me - The only thing worse than Braveheart's opening line is a documentary that completely ignores the facts. You could probably substitute in any of Michael Moore's "documentaries", but Roger & Me strikes me as worse than the rest because the climax of the film--Moore being cut off at a stockholder meeting--was a total fabrication.