I'm going to be splitting these up for spacing reasons so I'll start with
Best and Worst: DC Movie Edition
Best:
Batman '66
People say Sin City was a literal adaptation of the comics but
this is the most faithful movie of a comic ever made. "Sometimes you just can't get rid of a bomb."
Superman
Changing Krypton (I agree with Planet Man on this)
Killing Jonathan Kent.
Taking away Superboy.
Luthor's plot. I mean giving the technology back then having Luthor build a robot or super weapon would've been atrocious but they gave Superman a reasonable threat that was totally within their limits. Plus Hackman was awesome.
Having Jor-El speak to Clark. It helps they had Brando but the concept was just great.
Superman 2
General Zod was a perfect choice when you think about it. Terrence Stamp made him probably the best comic movie villain outside of Ledger's Joker and McKellan's Magneto.
Lois being proactive in figuring out Superman's identity. I always thought that Lois should know he's Superman before he tells her and they came close with this. This was one of the few things Smallville did right. Though in the Donner Cut where she just shoots him is pretty perfect and totally in character for Lois.
Batman and Batman Returns
Even though I think the plots and characters sucked Tim Burton did a great job making Gotham feel like a real city. The mixing of film noir with modern technology (well for 1989) worked great. Plus the score.
Batman Forever
The entire origin story and costume (sans nipples) of Robin was great and I liked Chris O'Donnell as him.
Jim Carrey playing it up as Riddler was great and I think he would've been leagues better than Nicholson as Joker. Plus his scheme was actually interesting.
I love how in this one they realized it was Batman '66 all over again (even though Burton's movies didn't) and just embraced it.
Switching from Keaton to Kilmer was a great choice.
Batman and Robin
At least Robin was good in this one again. Clooney was funny in an unintentional way.
Batman Begins
There's not much I can't say I didn't like about this. Making Jim Gordon, Alfred and Lucias Fox major players probably being the best part.
Batman's gadgets were great, especially the bat sonar scene.
Christian Bale's performance as Bruce and Batman were perfect and I could believe that no one would associate the two (as opposed to Keaton who really seemed creepy the entire time as Bruce)
Superman Returns
Brandon Routh's Clark was great as was Jimmy. This isn't really a change I just thought they were really good and wish they'd had a better script to work with.
Putting in pure "Superman Moments". This might have lacked in action but you had Superman saving a plane, stopping a bank robbery with a smile, saving a breakaway car, listening in on people to save, lifting a yacht and saving the Daily Planet which were all awesome. Sure the climax blew but hey you had a lot of times where you saw Superman being Super.
The Dark Knight
I of course have the usuals like Joker "making" Two-Face, Two-Face dying, Scarecrow returning, etc.
The Bat Pod makes so much more sense than any Batmobile Bruce has ever had. I hope they keep it in the sequel.
The "Bat-Men" vigilantes were a great spin and something that would actually happen in real life.
I know this isn't a change but still, "Not killing Joker" is perfect in contrast to killing Dent.
Watchmen
The costume changes were all pretty great with the exception of Ozymandius's. It's not the nipples or anything it just seemed like he looked like a villain from the get-go which ruins the ending.
The action scenes were really done great while not taking away from the realism of it. Sure Night-Owl and Silk Spectre were a little too in shape but people don't tend to forget moves like that. (And it made sense that Ozy would have such an easy time taking them down later on).
Worst:
Superman
Superman's extra powers. The entire turning back time thing was rediculous. The same goes for the "Super-Kiss" and "Super-Latex-Shield-Thingy" in the second.
I thought Reeve was a bit too bumbling as Clark. I thought Brandon Routh and even Tom Welling played better Clark Kents. Though Reeve still was the best Superman ever.
Luthor wearing wigs. It's just stupid that a character like Luthor wouldn't revile in his own physical look. He'd play it as a strength, not hide it.
Luthor's henchmen were horrible.
Superman 2
Some of the slapstick moments were horrible. It's not a comic change but firing Donner was their biggest mistake and his parts were easily the reason this one is so good.
Superman losing his powers and getting it on with Lois. It really was unnecessary though I can see where they were going with it.
Batman and Batman Returns (I'm biased because I hate the Burton movies)
Showing the Joker's origin plus making him Bruce's parents murderer (people ***** about it in Spider-Man 3 but never this one which I don't understand)
Batman killing people.
Really Penguin's entire plot in the second.
I could go on with many more but Chris Sims sums it up pretty well in his articles on the movie.
Batman Forever
Replacing Billy Dee with Tommy Lee. Seemed unnecessary but with the tone they had I think it worked.
All that neon.
Batman and Robin
Too hard to nail one down so I'll just say FreezeIvyBane.
Batman Begins
The tumbler turned me off a bit.
I wanted a lot more "Scarecrow moments" if you can understand what I mean.
Rachel Dawes was just horrible. I also agree with Gothamite that they should've used a character name from the comics. I mean they had Flass and Loeb it shouldn't have been too hard.
Superman Returns
Not tying it to the comics but to the movies. I mean you had Birthright at your disposal and you made Superman a deadbeat dad instead. I loved the originals but you've got to separate them. The saddest part is Singer could've made a great Superman origin movie with the right script but now we have Zak Snyder's questionable skills to look forward to.
As opposed to the first two Luthor's plot was horrible in this one. This isn't a knock on Spacey at all who I thought was great but his plot really didn't make any sense.
Lois also didn't seem to do any reporting in this one. Shame as she's one of my top ten favorite comics characters ever.
The Dark Knight
The sonar was kind of lame and one of the reasons it was kept out of the Oscar running honestly.
If I had to nail down one problem with the costume it was the symbol. Not that it didn't have the yellow background (I think a gold one matching the belt would've worked though) but that it was small and bent and meaningless compared to the rest of the suit.
Watchmen
Really Snyder's use of gore in these kinds of movies is getting excessive. Sure it was perfect in 300 but I don't want to see people's bones breaking through their skin. Moore insinuated at the violence perfectly and knew that sometimes less is more (no pun intended

)
This is something that they should've changed. The lynx. Get rid of it in a movie confusing as this.
Jonah Hex
Really everything. Mysticism being the main word coming to mind.