First, to answer your question about these specific instances, the correct formulations would be :

C’est ma réaction chaque fois que je la vois, CE QUI est toujours …

La raison pour laquelle j’aime cet arbre plutôt que l’autre c’est parce que cet arbre a des fruits, CE QUE n’a pas l’autre arbre.

To speak more generally, ce que/ce qui are used like que/qui, only when there is no expressed antecedent ; for example, they’re used to refer to an idea. In your second example, the idea is "the ability to bear fruits".

Then the choice between using que/ce que or qui/ce qui will depend on the grammatical function they occupy in the sentence. que is used when serving as the direct object ; qui is used when serving as the subject.

In your second example, we’re using ce que because the pronoun is the direct object. If we were to replace the pronoun, it would be as follows :

L’arbre n’a pas [la faculté de produire des fruits]

These two links can provide you with more info if needed : link and link

Hope it helps.