WMG / Super Mario Galaxy

Dusty Dune Galaxy is the site of an Apocalypse How.
Like Atlantis, a prosperous civilization once thrived on that planet and its assorted mini-moons. They built pyramids, monuments, and even orbiting space-temples with their own gravity. Then, like Atlantis, some sort of disaster struck and and all the earth in that region started turning to quicksand, driving the inhabitants to extinction. By the time Mario visits, only a few scattered ruins and barely-functional automated defense systems are left as a testament to the builders' great achievements.

The events of the Luigi playthrough happen in Luigi's imagination.

After returning from his adventure, Mario eventually gets around to telling Luigi about what happened. Later, while either dreaming or daydreaming, or possibly even during Mario's storytelling, Luigi plays out the story in his head, except he replaces Mario with himself doling out the heroics. He apparently doesn't put too much effort into making the dream believable though, since he still ends up rescuing "Luigi", there's only sparse unique dialog concerning Luigi, and Bowser considers second-banana, gets-lost-finding-stars, probably-afraid-of-his-own-shadow Luigi as much of a legitimate threat as Mario himself.
  • Alternatively, the Luigi playthrough is the version of events that occur in the heavily altered universe seen at the end of the game.

Kamella is Kammy Koopa

They do look alike, don't they? Kammy (which could be short for "Kamella") could be harnessing the energy of the Power Stars to battle Mario in a Super Mode.

Black Doom is Rosalina's brother

After finding out about his sister's journey into deep space, he started out on his own journey to find her. However, the aliens he encountered were not as friendly as the Lumas. These were the Black Arms, a murderous race of conquerors. He fought tooth and nail against these beasts, but even he fell to them after a long battle. The dying leader, impressed with this human's resilience and fighting prowess, saved his life by reconstructing his body into that of a new leader of the Black Arms. Afterwards, the leader died, leaving the reconstructed human to lead as Black Doom.

Since then, he lead the Black Arms in a sick parody of Rosalina's life among the Lumas. Instead of nurturing them to grow, he ordered them to kill and pillage. Instead of peace, he promoted war. And instead of birth, he believed the most in death. And when the Comet Observatory finally makes contact with the Black Comet, there is no telling what will happen when brother and sister are reunited.

In the storybook, the girl's father and brother neglect her and are possibly abusive

Her mother was nice to her, but did little to help her. The girl portrays them somewhat affectionately, but that's because she wanted to make the story appropriate for young Lumas. The neglect and possible abuse explains why she initially had no problems with leaving her family behind to look for the Luma's mother. When she cries for her dead mother, it's because she has realized that her mother wanted to help her, but was too afraid of the abusers. The girl doesn't miss her abusers, which explains why she doesn't cry for them when they're probably dead.

Rosalina is the daughter of Mario and Peach from another iteration of the universe

Rosalina's appearance is very similar to Peach's. Plus, the extreme closeup of Rosalina's mother has Peach's hair and earrings. Furthermore, in the French version, there is an extra page at the end of the storybook that mention her father and his mustache. Her phrasing at the end makes it clear that this isn't Rosalina's first trip to another universe either. The real reason she helps Mario is so that she doesn't lose her mother again.
  • Or conversely Rosalina's mother is Peach, but her father is Luigi. Evidence is that one of her keepsakes is her father's telescope. Mario doesn't have a telescope, but Luigi does. Also, in the storybook, her brother has a green hat. Also, Rosalina is tall, just like Luigi.
    • Having a telescope and being tall doesn't necessarily mean Rosalina is related to Luigi. Also, there's tons of people in the world who have lookalikes and not be related at all. It's called Identical Stranger and Peach and Rosalina might not be an exception to that. And the part about the father having a mustache, that's ONLY in the French version. You'd think they would include that detail in other versions if it was so important.

Star Bits grant you immortality.

Or at least a very long lifespan. How else would you explain why Rosalina looks to be around Peach's age, despite being hundreds (if not) thousands of years old?

Super Mario Galaxy is the last game in the "main" timeline.
In many of the Mario platformers, Mario and Bowser are sworn enemies and Bowser is legitimately threatening. However, in other games (particularly spinoffs), they're almost friends and Bowser is comic relief.

When the universe restarts at the end of the game, Bowser doesn't glare at Mario/Luigi at all, instead falling on his back clumsily and looking up. Both enemies and friendly NPCs are seen dancing and hanging out with no ill intent towards each other.

All the spinoffs - and maybe even a few mainline platformers like 3D World and Galaxy 2 - take place in the new universe where Bowser and Mario aren't really sworn enemies, but are at worst indifferent towards each other. Bowser tries to keep up a villainous image, slowly sinking to the point where the worst thing he does is crash Mario's parties, before finally giving up and going to their kart racing tournaments.

The reason Rosalina is called "Rosetta" in Japan...

...is because to Japanese people, the pronounciation of the name "Rosalina" would have been too ambiguous ("Rosalina"? "Rosarina"? "Loselina"? "Losarina"?), so a variation of her name that was less ambiguous was used for the Japanese release.note 

Dark Matter was an experimental attempt to create a hazard that can permanently kill Mario
Bowser thought that maybe if he could utterly disintegrate Mario at the molecular level, he might bypass all the extra lives and keep Mario from coming back. It didn't work, obviously, which is why it's never seen again after that one level — it's probably more expensive to make than good old fasioned lava, so no point to keep making it if it doesn't kill him better than anything else.