I'm just trying to give a partial solution to the second question.
Those examples had been mentioned in the previous posts. That is, finding manifolds which are open interiors of compact manifolds with boundary. This direction is natural since there are classical results regarding embedding compact manifold into Euclidean space of sufficient high dimension. So, for open manifolds, if they can be compactified such that the resulting spaces are compact manifolds with boundary, then classical results apply. However, examples provided here include manifolds with noncompact boundary, i.e., manifolds with uncountably many ends. Most of the results can be found in the joint paper with Guilbault https://arxiv.org/abs/1712.05995.
Here I just wanted to make a quick summary.
An $m$-manifold $M^m$ with (possibly empty) boundary is completable if there exists a compact manifold $\widehat{M^m}$ and a compactum $C \subseteq \partial \widehat{M^m}$ such that $\widehat{M^m}-C$ is homeomorphic to $M^m$. In this case $\widehat{M^m}$ is called a (manifold) completion of $M^m$. One can change the homeomorphism to diffeomorphism or PL homeo. for other categories.
Dim = 0,1 are obvious.
Dim = 2, we can't find a complete classification in the literature, so we provided a theorem in that paper. That is, a connected 2-manifold is completable iff it has finitely generated first homology. This is mainly based on classical work of Kerekjarto and Richards.
Dim = 3, it's mainly due to Tucker, where he showed that a
3-manifold can be completed if and only if each component of each clean neighborhood
of infinity has finitely generated fundamental group.
Let me talk about dimensions $\geq 6$ first. Then I'll go back to dimensions 4 and 5. The first breakthrough regarding this problem was due to Siebenmann in 1965. In his PhD thesis, he proved that an open n-manifold $M^n$ is completable (it was called collarable by that time) iff
(1) M is inward tame, (2) the end is pro-$\pi_1$ stable and (3) the Wall finiteness obstruction of the end vanishes.
In 1983, O'Brien generalized the theorem to one-ended manifold with possibly non-empty boundary.
In our paper, we dropped the O'Brien's assumption on that manifolds are one-ended. By properly generalizing Siebenmann's conditions, we proved that manifolds of dimension at least 6 are completable iff they are inward tame, peripherally $\pi_1$-stable at infinity, of zero Wall and Whitehead torsion. Our proof is based on PL manifolds, but one can employ standard techniques such as "rounding off corners" to handle the other catergories.
Our theorem is still true in dimension = 5 provided that the fundamental groups are good in the sense of Freedman and Quinn.
The theorem fails in dimension = 4. Kwasik-Schultz and (independently) Weinberger discovered that there are open 4-manifold satisfying Siebenmann's condition but fail to be collarable.
Just a quick comment on Ian's reference to a contractible open manifold $M'$ constructed by Kister-McMillan which doesn't embed in $S^3$. The example was first proposed by R. H. Bing. Haken further proved that $M'$ doesn't embed in any 3-manifold using his finiteness theorem. Recently, I showed that $M'$ can't be embedded in any compact, locally connected and locally 1-connected metric space. https://arxiv.org/abs/1809.02628
Edit As Ben McKay pointed out, my previous writing might cause confusion. So, some clarifications has been added.
Another direction to tackle OP's question is to embed manifolds into compact manifolds of same dimension. I think the 2-dimensional case of the second question is tractable via Ian Richards' classification of noncompact surfaces. That is, we need to exclude surfaces of infinite genus and infinite degree of nonorientability.
For higher dimensions, although exotic contractible open manifolds like Whitehead manifold and Davis' manifolds do embed in spheres, a classification is harder even for contractible open manifolds in general like the one mentioned in Ian Agol's answer. For a futher discussion in this direction, see a question posted by myself.