Michael,

- the existence of a well-founded $M$ and an embedding $j:V\to M$ different from the identity

is *equivalent* to

which is equivalent to

- the existence of an $\omega_1$-complete non-principal ultrafilter,

which is equivalent to

- the existence of a non-principal ultrafilter ${\mathcal U}$ such that the model $M$ obtained by taking the ultrapower by ${\mathcal U}$ is an $\omega$-model, i.e., the natural number of $M$ are isomorphic to the natural numbers.

This means that we really cannot say anything special along these lines about the ultrapower unless we are in the presence of measurable cardinals. (On the other hand, the ultrapower $M$ by an ultrafilter ${\mathcal U}$ on a set $\kappa$ is always an elementary map, so $M$ is elementarily equivalent to $V$ and, for each $V$-cardinal $\lambda$, the sets $\lambda^\kappa/{\mathcal U}$ are still linearly ordered (by dominance a.e.), even if ill-founded.)

Of course, if we relax conditions then we can actually say a great deal. For example, the existence of $0^\sharp$, a significantly weaker assumption than a measurable, ensures an embedding from $L$ to itself, or equivalently, an "$L$-ultrafilter" $U$ such that the *internal* ultrapower of $L$ by $U$ is well-founded.

Many large cardinal notions weaker than measurability can also be described in terms of elementary embeddings, though typically these are embeddings where the source and the target are (well-founded) sets rather than proper classes. The best known example of a large cardinal notion admitting such a characterization is weak compactness:

$\kappa$ is weakly compact iff $\kappa$ is strongly inaccessible and for
every transitive $M$ such that $\kappa\in M$, ${}^{<\kappa}M\subseteq M$, $|M|=\kappa$, and $M$ models enough set theory there exists an elementary embedding $k:M\to N$ where $N$ is a transitive set and ${\rm cp}(k)=\kappa$.

The existence of elementary or "partially elementary" embeddings between transitive sets is in general something that requires no assumptions beyond ZFC. For example, you obtain such embeddings by inverting transitive collapses of elementary hulls. Also, such embeddings guide the construction of square sequences in $L$.

If you relax the condition that the embedding and the ultrafilter live in $V$ and allow them to exist in some forcing extension $V[G]$, then (consistently) we can have well-founded $j:V\to M$ where the critical point is $\omega_1$, for example. Also, we can this way obtain embeddings where $M$ is an $\omega$-model, but not well-founded.

This is actually useful. Silver's original proof that SCH holds if it holds at singulars of cofinality $\omega$ proceeded by comparing $V$ and an $M$ as in the last paragraph (this idea led to the Galvin-Hajnal results on exponentiation that, in turn, led to pcf theory). The technique of generic embeddings has since proved to be very fruitful.

I recommend that you take a look at the articles by James Cummings and Matthew Foreman in the Handbook of Set Theory for *much* more on this subject.

That being said, the absence of measurability or "significant" large cardinals does not mean that different ultrafilters give us virtually indistinguishable ultrapowers $M$. In fact, Shelah's impressively fruitful pcf theory begins by looking at the cofinality (in $V$) of the ordered sets $\lambda^\kappa/{\mathcal U}$, and there is still much to explore here.