Classification problem for non-compact manifolds Background
It is well-known that the compact two-dimensional manifolds are completely classified (by their orientability and their Euler characteristic).
I'm also under the impression that there is also a classification for compact three-dimensional manifolds coming from the proof of the Geometrization Conjecture and related work.
Unfortunately for $n\ge4$ no similar classification is possible because it can be shown that it is at least as hard as the word problem for groups. Thus for higher-dimensional manifolds we instead focus on classifying all the simply-connected compact manifolds.
My question
Why in these "classification problems" are we only considering compact manifolds? Is there an easy reason why we restrict ourselves to the classification of compact manifolds? Does a classification of general (not necessarily compact) manifolds follow easily from a classification of compact manifolds?
 A: I just wanted to mention that the fact that the word problem is "hard" for groups doesn't mean that there can be no classification for manifolds of dimension $\geq$ 4.
The problem is that the word "hard" here means "there is no algorithm to solve it".  There certainly could be (though I'd doubt it) a relatively short list of invariants for n-manifolds which classifies them up to diffeomorphism.  The problem then becomes determining, for two specific manifolds $M$ and $N$ whether or not their lists of invariants are isomorphic/equal, which could be "hard".
For a somewhat trivial example: in dimension 2, compact manifolds are classified up to diffeomorphism by their first homology group.  This is a true (and useful) statement regardless of how "easy" it is to determine if $H_1(M)$ and $H_1(N)$ are isomorphic.
Further, if one wants to, say, apply the Heawood conjecture for compact surfaces, and one only knows $H_1(M)$, one needs only demonstrate it's NOT isomorphic to 0 or $\mathbb{Z}\oplus\mathbb{Z}/2\mathbb{Z}$, not isolate precisely which group it IS isomorphic to.
A: To illustrate both sides of all of the above comments (non-compact builds on compact, vs. non-compact is much harder than compact), I point out that ALL connected, separable, metric 2-manifolds (with or without boundary) meaning all connected, separable, metric spaces in which every point has an open neighborhood homeomorphic to the closed 2-disk have been classified.  See Brown, Edward M.; Messer, Robert: The classification of two-dimensional manifolds.  Trans. Amer. Math. Soc. 255 (1979), 377–402.  MR0542887 
The point is that the analysis is rather delicate and has some surprises, showing that the non-compact case does not follow easily from the compact.  Given the examples in dimension 3 by McMillan mentioned by algori, one of the surprises is that it could be done at all.
A: I have no access to Jstor right now, so I rely on my memory and, well, you may want to check all this.
Ian Richards theorem says that non-compact surfaces (without boundary) are classified by their orientablility, their genus (possibly infinite) and a triple of spaces, each one embedded in the preceding, that are: 


*

*the space of its ends, 

*the space of its ends with genus, 

*the space of its unorientable ends.
The space of ends is constructed by taking an increasing sequence of compact subset that cover a topological space $T$, and looking at the connected components of their complements. An end of $T$ is an infinite, decreasing sequence of such connected components. The point is that you can do that in a way that does not substancially depend on the sequence of compact you chose.
For example, $\mathbb{R}^n$ has only one end provided $n\ge2$ (look at the sequence of balls of integer radius and centered at some point), while $\mathbb{R}$ has two ends. The space of ends of a regular tree is a Cantor set.
An end is said to have genus if the connected components that define it all have genus (they never reduce to annuli). An end is said to be unorientable if the connected components that define it all are unorientable.
Now, consider the surface $S^n$ ($n=1,2$ or $3$ defined as the boundary of a tubular neighborhood of the usual embedding of the usual Cayley graph of $\mathbb{Z}^n$ into $\mathbb{R}^3$ (for $n=1$ you get a cylinder; for $n=2$ some sort of grid; for $n=3$ it is sometimes called a jungle gym). $S^2$ and $S^3$ are the surfaces described by Richard Kent in his third paragraph.
These two surfaces have exactly one end which is orientable but has genus. Therefore they all are homeomorphic. This is a pretty incredible result in my opinion. The most simple presentation of this surface is called the Loch-Ness monster: it is constructed by adding to a plane a sequence of handles placed in a row.
A: In a sense you more or less know what non-compact manifolds must look like provided you have a classification of the compact manifolds.  The starting point is the basic observation (Whitney) that a non-compact manifold has a proper function $f : M \to R$.   So the preimage of the intervals $[-n,n]$ for $n=1,2,3,\cdots$ form a nested family of compact submanifolds of $M$ that exhaust the manifold -- provided $f$ is transverse to the integers, which can be accomplished.  
So understanding $M$ boils down to seeing how the features of this family of submanifolds "pile up", and putting some sort of reasonable ideal boundary on $M$ -- since "ideal boundary"  is a lower-dimensional phenomenon, in principle you might be inclined to think this is reasonable.   
Of course I'm being pretty vague but it sounds like you were looking for something like this?
On the other side of things, because of the above non-compact manifolds are decidedly less combinatorial objects.  You don't have finite, combinatorial descriptions.  Larry Siebenmann shows people the example of the smooth structure on $I \times \mathbb R^4$ such that the projection map $I \times \mathbb R^4 \to I$ is a smooth submersion, but for which the fibers a pairwise non-diffeomorphic $\mathbb R^4$'s.   
A: Especially if you're looking at smooth manifolds, there's some weird stuff that happens in the noncompact case. The most famous example is the existence of infinitely many manifolds that are homeomorphic but not diffeomorphic to R^4. 
I don't know that similarly weird things happen just for topological manifolds, but I wouldn't count it out.
I guess it's worth mentioning, though, that plenty of utterly crazy things happen even for compact topological 4-manifolds. For instance, you have the E8 manifold, which isn't triangulable, and on the other end you have manifolds that admit way too many piecewise linear structures. This weirdness disappears for compact manifolds of higher dimension (fortunately), but for non-compact manifold you have to deal with stuff like R x E8, which I suspect isn't much nicer.
A: Complementing Ryan's answer: as shown by McMillan (Transactions AMS 102, 373-382) there is a continuum of pairwise nonhomeomorphic contractible open subsets of $\mathbf{R}^3$. So classifying noncompact manifolds in general is probably hopeless and some restrictions are necessary (e.g. one can consider only the interiors of compact manifolds with boundary that satisfy some conditions on the fundamental groups etc).
A: This answer complement the answers of Henry and Algori. I think, it is worth to strees, that a classification of open manifolds does not follow from a classification of compact manifolds. Open surfaces were classified, but open 3-folds are not, their classification does not follow from the classification of compact ones at least at the present time. In particular, {\it prime decomposition}, or Kneser's theorem (http://en.wikipedia.org/wiki/Prime_decomposition_(3-manifold)) does not hold for non-compact 3-manfiolds. There is a constructiion  due to Scott (http://plms.oxfordjournals.org/cgi/pdf_extract/s3-34/2/303) of an example of a simply connected 3-fold that can not be a connected sum of finite or infinite number of prime manifolds.
Open 3-manifold are actively studdied now. Let me give two citations that confirm further that our knowlage of compact 3-manfiolds is not sufficient for understending of non-compact ones.

1) Ricci flow on open 3-manifolds and positive scalar curvature.
Laurent Bessi`eres, G´erard Besson and Sylvain Maillot.
http://arxiv.org/PS_cache/arxiv/pdf/1001/1001.1458v1.pdf
Thanks to G. Perelman’s proof of W. Thurston’s
Geometrisation Conjecture, the topological structure of compact 3-manifolds
is now well understood in terms of the canonical geometric decomposition.
The first step of this decomposition, which goes back to H. Kneser,
consists in splitting such a manifold as a connected sum of prime 3-manifolds,
i.e. 3-manifolds which are not nontrivial connected sums themselves.
It has been known since early work of J. H. C.Whitehead [Whi35] that the
topology of open 3-manifolds is much more complicated. Directly relevant
to the present paper are counterexamples of P. Scott [ST89] and the third
author [Mai08] which show that Kneser’s theorem fails to generalise to open
manifolds, even if one allows infinite connected sums.

The refference for the article of Maillot is the followning.
2) Some open 3-manifolds and 3-orbifolds
without locally finite canonical decompositions. http://arxiv.org/PS_cache/arxiv/pdf/0802/0802.1438v2.pdf
Here is the citation

Much of the theory of compact 3-manifolds relies on decompositions into
canonical pieces, in particular the Kneser-Milnor prime decomposition [12,
16], and the Jaco-Shalen-Johannson characteristic splitting [10, 11]. These
have led to important developments in group theory [22, 7, 9, 24], and form
the background of W. Thurston’s geometrization conjecture, which has recently
been proved by G. Perelman [19, 20, 21].
For open 3-manifolds, by contrast, there is not even a conjectural description
of a general 3-manifold in terms of geometric ones. Such a description
would be all the more useful that noncompact hyperbolic 3-manifolds are
now increasingly well-understood, thanks in particular to the recent proofs
of the ending lamination conjecture [17, 4] and the tameness conjecture [5, 1].
The goal of this paper is to present a series of examples which show
that naive generalizations to open 3-manifolds of the canonical decomposition
theorems of compact 3-manifold theory are false.
A: I don't think there is an easy reduction to the compact case.  For instance, the Whitehead manifold is a non-compact, contractible 3-manifold which is not homeomorphic to real 3-space.  This suggests that the non-compact situation in 3 dimensions is much worse than the compact one (which, as you point out, is now fairly well understood, after a LOT of work).
