Cave Story/Wii versions

The US Wii version was released on 2010. The changes made from the PC version were rather rushed. The graphics were upscaled and just fine tuned here and there, the music was re-mastered, but not thoroughly quality-checked, and the extra game modes are available from the start.

Then came the PAL version, released on 2010. It changed quite a bit, being that the biggest changes are graphics that were refined even further, improved music quality and unlockable modes.

General

 * Every time the item screen or teleporter destiny screen is opened, the background goes black. This has been fixed in the PAL release.

Face
Message box portraits.

The character portraits suffered a lot of changes. Everyone got some small details, but some changed a bit more than that from the US to the PAL version. Some of the black pixels weren't assigned correctly and are actually transparent.
 * Sue got more divided eyelashes.
 * Balrog got some smudges and an eyebrow.
 * Jack lost his indecisive smile and became a cat.
 * Kazuma got a few more smudges and lost his small smile.
 * Jenka's nose... grew, apparently.
 * Misery cut her hair a bit, and got curly hairs on her forehead. Also, her earrings are red, her happy expression looks more insane, and her angry expression looks more intense (or is it less? I can't really tell).
 * Booster's lower teeth are showing.
 * Curly got an extra eyelash, more hair on the side of her head, and is blushing in all portraits.
 * The Doctor only shows his lower teeth, as opposed to a full grin, and got a dragon engraving on his Crown.
 * Balrog's shocked expression has him crying 2 tears of different colors... In none of the times Balrog uses this face is he really in any pain. They realized this and removed the tears in the PAL version.
 * The old robot's chin was redrawn, and some lighting was added to make it look shiny.
 * Quote's portrait (previously unused) changed a lot, from being a crudely edited Sue to looking more like an actual robot.
 * Itoh gained a few hairs, and raises his paw in the PAL version.
 * Ballos' face is a lot more wrinkled and cracked.

TextBox
HUD.

The answer box is smaller in the PAL version, and "YES" and "NO" are separated by a dot; it's a slash in the US version. The red numbers and bars are darker in the PAL release.

NpcAlmo1
The Core.

The eyes/lights are rounder in the PAL version.

NpcCemet
Cemetery enemies.

The big Pignon's hurt sprite has a drop of sorts in the PAL version, but it looks more like a bell in the US.

Ma Pignon's eyes are less triangular in the PAL release, except for his happy sprite, which makes them even more triangular. The small mushrooms in the graveyard have the same changes.

NpcCurly
Curly Boss Battle.

The Colons' eyes are squarer in the PAL version. Curly's mouth is slightly bigger, and in a few sprites, changed to make her happy, as opposed to confused. The teeth for the lying Colon have been removed in the PAL version's left sprite. Finally, Curly's missile shield is copy-paste-flipped for the right-facing sprite in the US version. This means that the reflection of the bubble has been flipped too. The PAL release fixes the reflection.

NpcGuest
General NPCs.

Several Mimiga, and the dogs, have their eyes changed, for when they are closed. They're a single pixel thick in the US version, and 2 pixels thick in the PAL. Kanpachi, the fisher, has more triangular eyes in the US version, while they're squarer in the PAL. Also, Chaco's eyes are slightly darker in a small area in the PAL version.

NpcKings
Balrog and Misery inside bubbles, used in the intro.

Balrog's scratches are less defined in the PAL version, and his mouth has also been smoothened. Misery's eyes are black in the US, dark blue in the PAL. The bubbles look smoother overall in the PAL release.

NpcMoon
Enemies in the Outer Wall.

The cat ghosts have small dots as eyes and simple lines as mouths in the US version. In the PAL, their eyes are circles, and their mouths are zig-zagged lines. The sprites where their eyes are closed are more anti-aliased in the PAL. The 2nd wool ball's sprite is a bit lower in the US version.

NpcRegu
General NPCs.

The colors of the robots in the Labyrinth have changed from being blue (standing) and red (deactivated) in the US, to green in the PAL. Some of the sprites of Quote escaping with Kazuma are changed by some pixels in the PAL version. For instance, Curly's head raises one pixel in one sprite the PAL, and some of the yellow costume's sprites have the stripe in the hat moved one pixel to the left in the PAL.

PrtLabo
The laboratory in the ending where Sue and Itoh are turned into humans.

The fans were changed to actually look like fans in the PAL version, instead of broken glass. An easy mistake to make, since the fan animation is only used in the end credits.

Credit01
Kazuma, Sue, and Quote escaping.

Kazuma's eyes are opened, Sue's mouth is fixed, and Quote is no longer smiling in the PAL version.

Credit02
The boss fight against the Core, Misery and Sue.

In the PAL release, some magic balls have been added, Sue got more distinctive fur and gained teeth, Quote has a drawing of Ikachan on the back of his hat, Misery's hair has been spiked a bit, and overall, more detail was added.

Credit03
The boss fight against Misery.

Bats were added, and Quote's face and leg were fixed in the PAL version.

Credit04
The rocket taking off in the Plantation.

Itoh's nose is shinier, he gained a small extra hair, and the rocket is blasting off with a sparkle in the PAL release.

Credit05
Climbing the Outer Wall.

For the PAL version, the cat was given a more appropriate cat mouth, as well as a nose, the yarn ball got a small yarn tail, and another cat has also been added to the picture. Quote's hat and the main cat's shadow were also fixed.

Credit06
Battle against Ironhead.

Quote's eyes and hat were retouched a bit, but mainly, several bubbles were added to the scene in the PAL version.

Credit07
Battle against Balrog before the Boulder is pushed.

In the US version, Balrog has no pupils nor scratches, and Quote doesn't have Ikachan on his hat. For the PAL version, the smoke and rockets were more detailed, Curly's eyelashes grew, her eyebrows got lighter, and her nose was centered better.

Credit08
Dr. Gero giving the key to the Clinic.

For the PAL version, a belt was added to Quote, Curly's face was retouched a bit, and a bookshelf has been added to her left.

Credit12
Balrog flying with Quote and Curly.

Quote looks more worried, the clouds have been enhanced a bit, and Balrog got a happier mouth and eyebrows for the PAL release.

Credit14
Quote and Curly in Hell.

Curly's eyebrows and mouth, and Quote's mouth were improved, and the angels in the background got eyebrows in the PAL version. Quote's chest and legs were changed a bit.

Credit17
Sue discussing with King and Jack.

The only addition to the PAL version was a rather important oversight: King doesn't have his scar in the US version. That is absent in the PC version as well.

Other changes

 * Misery's eyes on the final boss battle against the core are 2 pixels thick when closed. In the US version, they're only 1 pixel thick.
 * Ballos, in his human form, has a red eye and a white eye. In the US version, his right-facing sprites are merely copy-paste-flipped, switching the positions of his eyes. This has been fixed in the PAL release.

Audio
The songs don't loop correctly in the US version, and the drums don't play at all. This has been fixed in the PAL version, but, then again, the entire soundtrack has been slightly redone for the PAL release.

The sound effects play a lot louder than the music in the US version. Nicalis even acknowledged this and recommended setting the sound effects' volume bar to 1/3.