Non-Hausdorff spaces appear naturally in the study of $C^*$-algebras. If $A$ is a $C^*$-algebra, we want to study $A$ by considering the space $X$ of primitive ideals of $A$, which we call its spectrum by analogy with algebraic geometry.
If $A$ is commutative, then every primitive ideal of $A$ is maximal and so $X = \operatorname{mSpec} A$, which is easily seen to be a compact Hausdorff space. Moreover, the functions on $X$ (in the sense of algebraic geometry, thus the elements of $A$ are in natural bijection with these functions) are exactly the functions $X \to \mathbb C$, since if $I$ is a maximal ideal of $A$, then $A/I = \mathbb C$. This cannot be the case for a noncommutative $A$ because one needs some "noncommutative functions".
Now if $A$ is noncommutative and $I$ is a primitive ideal of $A$, then $A/I$ is a simple $C^*$-algebra (i.e. a $C^*$-algebra which is simple in the sense of noncommutative rings, thus $A/I$ has no two-sided ideals), and so does not have to be a field. Often $A/I$ is a matrix ring such as $\mathbb C^{2 \times 2}$. As a consequence, there is no longer a guarantee that $X$ is Hausdorff.
One of my favorite examples of a non-commutative spectrum of a $C^*$-algebra arises from considering the action $\varphi$ of the group $\mathbb Z/2$ on the unit circle $S^1 = \{(x, y): x^2 + y^2 = 1\}$ by reflection across the $x$-axis $\{(x, 0)\}$. Now $C(S^1 \to \mathbb C)$ is a $C^*$-algebra consisting of functions on $S^1$, and $\varphi$ induces an action of $\mathbb Z/2$ on $C(S^1 \to \mathbb C)$. Whenever we have a group acting on a $C^*$-algebra we can take the semidirect product of the group and the $C^*$-algebra to get a new $C^*$-algebra.
Let $A$ be the semidirect product of $\mathbb Z/2$ and $C(S^1 \to \mathbb C)$. One can think of the spectrum of $A$ as the quotient of $S^1$ by $\varphi$, which gives the line segment $[-1, 1]$ obtained by deleting the $y$-coordinates of $S^1$. But there are two funny things about this line segment.
First, the functions on $\operatorname{Spec} A$ are noncommutative, and in fact are functions $\operatorname{Spec} A \to \mathbb C^{2 \times 2}$.
Second, not every function $\operatorname{Spec} A \to \mathbb C^{2 \times 2}$ appears in $A$. Indeed (up to a choice of isomorphism), one can show that every function $f: \operatorname{Spec} A \to \mathbb C^{2 \times 2}$ in $A$ satisfies $f(\pm 1) = \begin{bmatrix}1 & a\\ a & 1\end{bmatrix}$ for some $a \in \mathbb C$. This corresponds to the fact that the action of $\varphi$ on the endpoints $(\pm 1, 0)$ of $S^1$ is trivial.
The ring $R = \{\begin{bmatrix}1 & a\\ a & 1\end{bmatrix}: a \in \mathbb C\}$ is not simple. In fact, there are two simple rings which are quotients of $R$. Thus there are two primitive ideals of $A$ corresponding to each of the points $\pm 1$. Thus those points are bug-eyed (in the same sense as the bug-eyed lined) and $\operatorname{Spec} A$ is not Hausdorff.