1.Merchants
What are they?

They're called Strangers.

2.Mystery Switch in FSC
It just stands there with no known use. I've tried doing the level pushing it and not pushing it. Nothing.

It actually makes a ghost box appear between some unbreakable blocks that you can only get witha gun, which clears a hidden path to 4 red treasure boxes. Some guy made a thread about this discovery about it some time ago, and a GM comfirmed his discovery.

3.Gremlins
How did they get there? Did they come from here, or from somewhere else?

Apparently, they are Cradle's natives. I think.

4.Knights
Think about it, what ARE we? all you ever see are our eyes...

Vanaduke, without his mask, looks like a SK. Maybe the SK used to live on Cradle, and stuff happened, so they left.

5.Alpha Squad
Where did they go, and how did they get there?
Into to Core. Maybe the diety in the Core let them in.

6.Mystery Symbols in Dark City
What are they for? They also appear around minerals in other areas.
THey're just runes. I think Teir 3 gremlins make stuff like that to heal people. Or maybe they have someting to do with crystls.

7. Crash of the Skylark
Why did it crash? What-or who-caused it to crash?
ENgine failiure. How, who knows?

8.Snarbolax
How does a beast like that live on a small floating are in the middle of nowhere?

MAGIC. Or maybe it eats the knights it kills.

It's there because, according to the Echo Stones from the sanctuary, different worlds were drawn together to form the clockworks. he may be from another world, and was stranded when he was sent there.

9.Almire
Who built it and what were the other 2 kingdoms told of in its lore?

I'm guessing the other 2 kingdoms are the Aurora Kingdom (Aurora Ruins is a type of place), but the other is unknown. Maybe the Order of the ROse or whatever that group that used to wear the Rose Regelia stuff was called.

10.The Core
What is in it? Who built it? What is this mysterious voice in the Snactuary saying it's in the core to be protected? For every question answered, more emerge.

Some kind of prison/sanctuary for a diety being chased by the Swarm. Methinks TInkinzar somhow built it.

I noticed while wearing a heavy demo helm that we have a nose shape! You have to rotate your character but look closely, so we must atleast have a shape :).

8. The snaroblax eats the wolvers that don't do it's bidding.

??) What happened to the Vog?

??) Where is the ancient Tortedrone?

??) Who is the ultimate boss of the Devilites?

??) Where did the Spiral Knights come from?

I'm gonna take a whack at this.

1.Merchants
What are they?

I believe they're what the SKs turned into after the disintegration of what is now Cradle. More on that...

2.Moorcroft
Why put a hotel in the middle of a planet? Plus it's for the undead...

It's just one of many interdimensional mistakes in the mess that remains of the galazxy that was once here.

3.Gremlins
How did they get there? Did they come from here, or from somewhere else?

The Gremlins are a post-destruction race of spacefarer freebooters that have been building Cradle into a floating Planet-ship. They are a third party to the tragedy of the Spiral Knights saga.

4.Knights
Think about it, what ARE we? all you ever see are our eyes...

Extra-dimensional residue. Essentially ghosts. We were all completely atomically erased from this plane, but, true to religion, our souls remained. The forces that were unleashed in the galaxial implosion changed the energy of these souls into something more substantial than an extradimensional echo.

5.Alpha Squad
Where did they go, and how did they get there?

They are an elite SK squad for sure, but Alpha Squad found their way to the center of the reason why the Gremlins are so covetous of Cradle, namely the singularity contained in the core.

6.Mystery Symbols in Dark City
What are they for? They also appear around minerals in other areas.

Markers placed there by one of the few factions trying to attain control of Cradle. Basically, they say "take this, it's good stuff"

7. Crash of the Skylark
Why did it crash? What-or who-caused it to crash?

It was meant to be. It was meant to crash to move the SK saga along. What is real is inconsequential, although it's really just a subconsciously accepted story to keep the SK knights returning to Cradle. The essence of the singularity calls to it's missing pieces, including the Knights of Almire and all that remains of them.

8.Snarbolax
How does a beast like that live on a small floating are in the middle of nowhere?

He's a feral Gremlin creature, like all the other creatures of Cradle. It's a mutant of the seeded species of Wolvers that are the predators of Cradle.

9.Almire
Who built it and what were the other 2 kingdoms told of in its lore?

Almire is where the SKs come from. We all were once under the banners of Almire, or the other two kingdoms. When the cataclysm happened, the kingdom's influence on the world and it's inhabitants kept it's concept alive, and we are left with twisted remnants of what once was the kingdom's grand fortresses.

10.The Core
What is in it? Who built it? What is this mysterious voice in the Sanctuary saying it's in the core to be protected? For every question answered, more emerge.

Gremlins built the housing when they found the singularity and the chaos that surrounded it. That's what the core is. What's inside is a collapsed galaxy, and within that, a million, billion souls who's memories and feelings created what is now Cradle when the core locked in place and effectively stopped the progression of the dimensional tear it was creating.

The singularity has attained a sentience and knows that it's consciousness relies on it being locked in this spot and time. The SKs want to open it and rejoin with it. Vanaduke has been reconstructed to block the path to opening the core.
The Shadow Lairs are a broken reflection of what Cradle is now. The deeper one goes into the Shadows, the closer they get to the core's consciousness. The core's misdirections won't last forever, however.

What actually happened between the spookats and the owlites? Back when the former probably weren't as spooky as they were kat.
Are mewkats perhaps the lost souls of occasional kittens accidentally killed alongside all the bigger kats? How much knowledge was lost with the wise owlite race?