@Mathias: Good point. Sorry if my original post isn't clear enough. Image below should help. I'm not referring to the technical nature of tiles as modular, but instead to the overall arrangement of the tiles as a single background image perceived to be various layers that, if indeed these "layers" were separate, could be added/replaced/removed/palette-swapped depending on the type of game level desired.
For example a sky level could consist of the two 'layers' in image row 0, col 1 in the image below, while a hill/plains level would consist of the 2 'layers' in image 0,0 and a mountainous level would be the 3 layers in 1,2 for example, and a hilltop level would be the 3 layers in 1,3).

As you can see, the sky "layer" is almost exactly the same in almost every image. the hills could easily be palette-swapped for a night time level, using a different sky of stars instead of clouds in the farthest BG layer (which is actually done in the game when Yoshi gets wings if I'm not mistaken, though this was the most illustrative example I could find).
What I'm trying to do is find a set of principles I can use to design unique-looking background 'layers' that aren't quite as generic-looking or cartoony as these, but still keep them modular enough (while maintaining some sense of consistent lighting / color-harmony that applies to less-surreal environments) that they can be combined with any other tilesets (in the playable area) and foregrounds.
Hope that explains what I'm trying to do a bit better.
Has anyone else done something like this before? If so, can you offer me some tips/ideas/rules-of-thumb on how to do it?
EDIT:
@RAV: Yeah, pretty close to what I was trying to say. Sky color is one layer, clouds are on another, thicker clouds are another, trees another, closer trees another, bushes another layer, and finally, the playable area, and then a foreground of some kind. Say you don't need trees in the distance, but you do need mountains, you just swap them out. You may still want bushes, though your trees closer to the bushes won't fight with the mountains and wont look out of place without the distant trees you replaced with mountains either, or better yet, they work in-addition to the mountains. That's what I'm going for.