Burnable bushes. Being the wrong color is so obvious, it only happens once. Instead, look at the markings on the bushes. There are only two patterns to the black pixels, burnable and not burnable. That means on a screen with a secret, it would be one bush that doesn't match the others. I find the bottom left triangle is the easiest thing to scan for, but burnable ones also look slightly darker since there are more black pixels.
Bombable cliff. This one is more obvious. A bombable spot has cracks, and they're in the same pattern each time. There are also a couple types of bombable rocks.
Pushable blocks will be easy to spot. Every pushable block has a flatter top, like the top of it got milled down. You can scan a room for it, instead of having to push each block, especially in a room with an unfamiliar block layout. Maybe the flat top cuts the weight down, or maybe I just needed a distinct visual effect and weight is just a convenient afterthought.
Bombable walls in dungeons are always marked the same, but it isn't always as noticable. The brick dividing lines are missing near the middle of the wall. Just look below the little pointy things. This is the case for necessary bombed walls and secret walls. Left is typical, right is bombable.
