Concerning question (1).
I became very interested in this question last year---obsessed with it, actually---when I found myself unable to prove that any of the natural-seeming examples were actually instances of incomparability (for example, none of the approaches suggested in the various comments actually work). After my numerous attacks on it failed, I began seriously to doubt the strong intuition underlying the question, that there should be incomparable models. Eventually, I was a able to show that indeed, any two countable models are comparable by embeddability. My paper is available at:
The main theorems are:
Theorem 1. Every countable model of set theory $\langle M,{\in^M}\rangle$ is isomorphic to a submodel of its own constructible universe $\langle L^M,{\in^M}\rangle$. Thus, there is an embedding $j:\langle M,{\in^M}\rangle\to \langle L^M,{\in^M}\rangle$ that is elementary for quantifier-free assertions in the language of set theory.
The proof uses universal digraph combinatorics, including an acyclic version of the countable random digraph, which I call the countable random $\mathbb{Q}$-graded digraph, and higher analogues arising as uncountable Fraisse limits, leading eventually to what I call the hypnagogic digraph, a set-homogeneous, class-universal, surreal-numbers-graded acyclic class digraph, which is closely connected with the surreal numbers. The proof shows that $\langle L^M,{\in^M}\rangle$ contains a submodel that is a universal acyclic digraph of rank $\text{Ord}^M$, and so in fact this model is universal for all countable acyclic binary relations of this rank. When $M$ is ill-founded, this includes all acyclic binary relations.
The method of proof also establishes the following, which answers question (1). Version 2 on the archive, which will become visible in a few days, cites this question and Ewan Delanoy.
Theorem 2. The countable models of set theory are linearly pre-ordered by embeddability: for any two countable models of set theory $\langle M,{\in^M}\rangle$ and $\langle N,{\in^N}\rangle$, either $M$ is isomorphic to a submodel of $N$ or conversely. Indeed, the countable models of set theory are pre-well-ordered by embeddability in order type exactly $\omega_1+1$.
The proof shows that the embedability relation on the models of set theory conforms with their ordinal heights, in that any two models with the same ordinals are bi-embeddable; any shorter model embeds into any taller model; and the ill-founded models are all bi-embeddable and universal.
The proof method arises most easily in finite set theory, showing that the nonstandard hereditarily finite sets $\text{HF}^M$ coded in any nonstandard model $M$ of PA or even of $I\Delta_0$ are similarly universal for all acyclic binary relations. This strengthens a classical theorem of Ressayre, while simplifying the proof, replacing a partial saturation and resplendency argument with a soft appeal to graph universality.
Theorem 3. If $M$ is any nonstandard model of PA, then every countable model of set theory is isomorphic to a submodel of the hereditarily finite sets $\langle \text{HF}^M,{\in^M}\rangle$ of $M$. Indeed, $\langle\text{HF}^M,{\in^M}\rangle$ is universal for all countable acyclic binary relations.
In particular, every countable model of ZFC and even of ZFC plus large cardinals arises as a submodel of $\langle\text{HF}^M,{\in^M}\rangle$. Thus, inside any nonstandard model of finite set theory, we may cast out some of the finite sets and thereby arrive at a copy of any desired model of infinite set theory, having infinite sets, uncountable sets or even large cardinals of whatever type we like.
The article closes with a number of questions, which you may find on my blog post about the article. I plan to make some mathoverflow questions about them in the near future.