I know, I'm sharing another game makers work by linking this, but I'm mainly doing it to share some work I've made, and because some of the ideas in the games I made are actually somewhat influenced by the Submachine games. The following are links to the forum topics for the levels. You'll need to install the game to play the levels, which you can get at:
http://nifflas.ni2.se/?page=Knytt+Stories
Here is my best level: The White City
http://nifflas.lpchip.nl/index.php?topic=5135.0
A related level (in the same universe) is A Vague Feeling
http://nifflas.lpchip.nl/index.php?topic=4907.0
I was going to do a whole series of games like this, slowly unwrapping the plot behind these two story lines, but I've twice lost all my custom made tilesets and maps.

And the final level I am quite proud of is Stone Tiers
http://nifflas.lpchip.nl/index.php?topic=3199.0
You can also see links to a few other levels I've made in my forum signature.
I also contributed to a community level called Endless Winter, and I'm quote proud of that work too. Everything middle to left in Lab 3 is mine, plus the above ground screens entering lab3 and to either side. I think you'll definitely see the Submachine influences there. XD I'll boast and say that there where no labs in this game until I made Lab 3, though someone else made the tileset and suggested we use it. XP XD
http://nifflas.lpchip.nl/index.php?topic=5648.0
And I can't help but suggest my favorite level: splitMind by Jigganis
http://nifflas.lpchip.nl/index.php?topic=3852.0
And look up anything by egomassive, who has made a great mod of the Knytt Stories game. Some of yoji's early work is interesting too.
AND, very exciting, a much awaited sequel to Knytt Stories called Knytt Underground was just released. XD XD XD
So, revisiting that forum, which I haven't participated in for a long time, makes me wish that Mateusz would release a kind of Submachine Game Maker which would let you make your own Submachine games using the backgrounds and objects from the games, make your own notes, and perhaps change the color scheme of objects and backgrounds. XD It doesn't seem like Mateusz's style to do that though.