Sometimes it helps to convert a question to a declarative sentence, as you try to figure out the tense of the verb.
Ask yourself what the subject of the clause is. Are there more than one? Is the subject singular or plural?
The tree is what color(s). The subject is "tree" (singular), not "colors" (plural); so it takes a singular verb, is.
What colors are in the tree? I know this is tricky. The tree is no longer the subject of the clause. "Tree" is object of the preposition, "in." In this case, "colors" (plural) is the subject of the clause, so we need the plural verb.
You can ask, "What colors are in the tree?" but you can't ask, "What colors are the tree?"
The "in" makes all the difference.
What color are the grass and the leaves?
The grass and the leaves are what color? (They're both green. Only one color.)
The subject of the sentence is "the grass and the leaves." There are two subjects so the "subject" is plural, calling for a plural verb.
You cannot say, "What color is the grass and the leaves?" I know it sounds right, but in my opinion it's wrong. "Color" is not the subject of the sentence, in this case!
If you're not sure what the subject of the sentence/clause is, you can't possibly be sure of whether the verb should singular or plural. 
There is this thing where you're allowed to call two things a single unit, IF that's the way you think of it.
(The house and garage are/is white.) What color are/is the house and garage?
I don't like it. 