The fixpoint A for B(x) shown to exist in the proof of the diagonal lemma is self-referential in the following sense: A has the form B(t), where t=#A is provable in T. It is only through the use of such self-referential formulas that we know that every B(x) in fact has a fixpoint.
Nevertheless, in the proof of Gödel's theorem, the fact that the Gödel sentence is self-referential is not used, but only the fact that it is a fixpoint for the predicate "x is not a theorem of T".