If you are talking about the physical universe (and why wouldn't you be, come to think of it), you might make the case that it is not an element of itself. This would work if a property of every set was that it is not a "physical object" however you may define it, and if the physical universe was the set of all physical objects. Likewise, it could be shown that the set of all non-physical objects is an element of itself.
Suppose that all sets are not physical objects.
$\forall x: [Set(x)\implies \neg P(x)]$
where $Set$ is the "is a set" predicate, and $P$ is the "is a physical object" predicate.
Suppose further that the physical universe is the set $U$ of all physical objects.
$Set(U)$ and $\forall x: [x\in U\iff P(x)]$
If such a set actually exists, we would have $\neg P(U)$ and, therefore, $U\notin U$.
Now, suppose that $U'$ is the set of all non-physical objects.
$Set(U')$ and $\forall x: [x\in U'\iff \neg P(x)]$
If such a set actually exists, we would have $\neg P(U')$ and, therefore, $U'\in U'$.
EDIT:
The trouble is, $U\cup U'$ is just the usual universal set of all things that, as I have shown in my previous answer, cannot exist in my system (or in ZFC). So, either $U$ or $U'$ or both cannot exist. Another paradox?