All countable ordinals are embeddable in $\mathbb{Q}$.
For "small" countable ordinals, it is simple to do this explicitly. $\omega$ is trivial, $\omega+1$ can be e.g. done as $\{\frac{n}{n+1}:n\in \mathbb{N}\} \cup \{1\}$.
$\omega*2$ can be done as $\{\frac{n}{n+1}:n\in \mathbb{N}\} \cup \{1+\frac{n}{n+1}:n\in \mathbb{N}\}$, and $\omega*n$ as $\bigcup_{i\le n} \{i+\frac{n}{n+1}:n\in \mathbb{N}\}$
That immediately also gives $\omega^2$ as $\bigcup_{i \in \mathbb{N}} \{i+\frac{n}{n+1}:n\in \mathbb{N}\}$
And going further is still relatively easy: We can biject the above embedding of $\omega^2$ onto a single interval $(0,1)$, e.g. through $f(x)=1-\frac{1}{x+1}$ since this is an order preserving bijection from $\mathbb{Q}^+$ to $(0,1)$, allowing us to get $\omega^2+n$, $\omega^2*n$ etc. And by iterating that process, we can get any ordinal below $\omega^\omega$.
But this sort of embedding fails at $\omega^\omega$ as the iteration of $f$ doesn't seem compatible with taking the infinite union - figuratively speaking, we'd squish things to $0$. So what would an explicit embedding of $\omega^\omega$ look like? And the question, then, is if it is possible to give an explicit embedding of $\epsilon_0$? Is the fact that Peano arithmetic cannot prove well-foundedness of $\epsilon_0$ an indication that it cannot be embedded by such elementary functions and their iterations?
And what about even bigger countable ordinals such as the Veblen ordinals, Feferman-Schütte, Bachmann-Howard? From its definition, even if the above all are possible, I assume that the definitive bound of where one can define an effective procedure for the embedding must be Church–Kleene - is that a correct conclusion?
Lastly, does the situation change when we use $\mathbb{R}$ instead of $\mathbb{Q}$, which would allow us to use, perhaps, more easily understood yet inherently complex functions?
Edited because $\omega^2 \neq \omega^\omega$