For the most part, what I'm doing isn't really any "secret sauce", and I guess it speaks well of Stencyl, but I'm mainly just using the basic concepts of logic building (if, then, attributes) and putting in artwork and designing a game. I've also probably picked up a few little tricks along the way, often by needing to do something and asking people how. Being goal-driven is the best way to learn Stencyl. What do you want to do? Break it down. What's your next objective? Find out how to do it. Have a *plan*. I'll tell you straight off I'm not particularly bright, I'm just motivated and stubborn have a firm idea of what I want to do. If you have the firm picture of what you want to do, then it's just a matter of connecting the dots. If each dot means asking the forum "how do I do this?" then so be it. There's no shame in that.
Anyway: The look of the game involves actors (I don't generally use tiles for anything other than setting the collision of the levels, for convenience, you don't actually see the tiles in my game) with layers of other actors on top of them. So there's kind of this blue-ish hue to the game that's in part from the original art, but also caused by a blue-tinted, grainy overlay (a big graphic) covering the screen with "multiply" blending mode.
What put it over the top for me were the inclusion of full screen shaders, which let me bump up the contrast, use a bit of bloom, and tweak the saturation. I found contrast and saturation go well together, because upping the contrast made for a more cinematic presentation, but it made some of the colors get a bit out of control, so using the saturation shader to roll things back a bit was nice.
You may have also noticed a slight "everything is moving for some reason!" quality to the game, which, I dunno, people may like or dislike. For me, I just like it, I dunno, it's a "just because" thing. Some feeling that everything is sort of subtly crawling and shifting around, just so, adds kind of this interesting "aliveness" to the game -- at least, to me. This is done, as Jon said, by way of the wave shader.
In short, if you want to know what the secret sauce is, I guess the closest thing to that description is "full screen shaders". Other than that, I'm not doing anything particularly ingenious.