Questions about analogy between Spec Z and 3-manifolds I'm not sure if the questions make sense: 
Conc. primes as knots and Spec Z as 3-manifold - fits that to the Poincare conjecture? Topologists view 3-manifolds as Kirby-equivalence classes of framed links. How would that be with Spec Z? Then, topologists have things like virtual 3-manifolds, has that analogies in arithmetics?
Edit: New MFO report: "At the moment the topic of most active interaction between topologists and number theorists are quantum invariants of 3-manifolds and their asymptotics. This year’s meeting showed significant progress in the field."
Edit: "What is the analogy of quantum invariants in arithmetic topology?", "If a prime number is a knot, what is a crossing?" asks this old report.
An other such question:
Minhyong Kim stresses
the special complexity of number theory: "To our present day understanding, number fields display exactly the kind of order ‘at the edge of chaos’ that arithmeticians find so tantalizing, and which might have repulsed Grothendieck." Probably a feeling of such a special complexity makes one initially interested in NT. Knot theory is an other case inducing a similar impression. Could both cases be connected by the analogy above? How could a precise description of such special complexity look like and would it cover both cases? Taking that analogy, I'm inclined to answer Minhyong's question
 with the contrast between low-dimensional (= messy) and high-dimensional (= harmonized) geometry. Then I wonder, if "harmonizing by increasing dimensions"-analogies in number theory or the Langlands program exist.    
Minhyong hints in a mail to "the study of moduli spaces of bundles over rings of integers and over three manifolds as possible common ground between the two situations". A google search produces an old article by Rapoport "Analogien zwischen den Modulräumen von Vektorbündeln und von Flaggen" (Analogies between moduli spaces of vector bundles and flags) (p. 24 here, MR). There, Rapoport describes the cohomology of such analogous moduli spaces, inspired by a similarity of vector bundles on Riemann surfaces and filtered isocrystals from p-adic cohomologies, "beautifull areas of mathematics connected by entirely mysterious analogies". (book by R., Orlik, Dat) As interesting as that sounds, I wonder if google's hint relates to the initial theme. What do you think about it? (And has the mystery Rapoport describes now been elucidated?)
Edit:
Lectures by Atiyah discussing the above analogies and induced questions of "quantum Weil conj.s" etc.
This interesting essay by Gromov discusses the topic of "interestung structures" in a very general way. Acc. to him, "interesting structures" exist never in isolation, but only as "examples of structurally organized classes of structured objects", Z only because of e.g. algebraic integers as "surrounding" similar structures. That would fit to the guesses above, but not why numbers were perceived as esp. fascinating as early as greek antiquity, when the "surrounding structures" Gromov mentions were unknown. Perhaps Mochizuki has with his "inter-universal geometry" a kind of substitute in mind?    
Edit: Hidekazu Furusho: "Lots of analogies between algebraic number theory and 3-dimensional topology are suggested in arithmetic topology, however, as far as we know, no direct relationship seems to be known. Our attempt of this and subsequent papers is to give a direct one particularly between Galois groups and knots." 
 A: From reading the Morishita article 0904.3399 (page 24), there is a following analogue of Poincare conjecture:

Suppose that k is a number field whose ring of integers $\mathscr O_k$ is “cohomologically 
  $\mathbb Z$”, namely 
  $${}^{c}H^{i}(\text{Spec}\, \mathscr O_k,\mathbb{Z}) = {}^{c}H^{i}(\text{Spec}\, \mathbb{Z},\mathbb{Z})$$
  for $i ≥ 0$. Then $\mathscr O_k$ must be $\mathbb Z$. 

A: It seems the following remarks in M. Kapranov's paper http://arxiv.org/abs/alg-geom/9604018
page 64 bottom, has not been mentioned so far

According to the point of view going
  back to Y.I. Manin and B. Mazur, one
  should visualize any 1-dimensional
  arithmetic scheme X as a kind of
  3-manifold and closed points x ∈ X as
  oriented circles in this 3-manifold.
  Thus the Frobenius element (which is
  only a conjugacy class in the
  fundamental group) is visualized as
  the monodromy around the circle
  (which, as an element of the
  fundamental group, is also deﬁned only
  up to conjugacy since no base point is
  chosen on the circle), Legendre
  symbols as linking numbers and so on.
  From this point of view, it is natural
  to think of the operators (algebra
  elements) af,x,d for ﬁxed f and
  varying x, d as forming a free boson
  ﬁeld Af on the “3-manifold” X; more
  precisely, for ±d > 0, the operator a
  ± f,x,d is the dth Fourier component
  of Af along the “circle” Spec(Fq(x)).
  The bosons a ± f,x,d and their sums
  over x ∈ X (i.e., the Taylor
  components of log Φ ± f (t)) will be
  used in a subsequent paper to
  construct representations of U in the
  spirit of [FJ].

It might be that recent paper by Kapranov and coauthors: 
http://arxiv.org/abs/1202.4073
The spherical Hall algebra of Spec(Z)
is somehow developing ideas quoted above.
The question which I heard from V. Golyshev and others many years ago is the following:
if Spec (Z) is analogous to 3-fold, what should be arithmetic analog of Chern-Simons theory ?
A: I cannot really say anything about relations with Poincare conjecture, but the obvious references you should look at are
M. Morishita. On certain analogies between knots and primes. Journ. f¨ur
die reine u. angew. Math., 550 (2002), 141–167.
(there is a more recent exposition also by Morishita in http://arxiv.org/abs/0904.3399 )
and Manin's "The notion of dimension in geometry and algebra": http://arxiv.org/abs/math/0502016 which contains abundant references inside.
A: The analogy doesn't quite give a number theoretic version of the Poincare conjecture.  See Sikora, "Analogies between group actions on 3-manifolds and number fields"
(arXiv:0107210): the author states the Poincare conjecture as "S3 is the only closed 3-manifold with no unbranched covers."  The analogous statement in number theory is that Q is the only number field with no unramified extensions, and indeed he points out that there are a few known counterexamples, such as the imaginary quadratic fields with class number 1.
The paper also has a nice but short summary of the so-called "MKR dictionary" relating 3-manifolds to number fields in section 2.  Morishita's expository article on the subject, arXiv:0904.3399, has more to say about what knot complements, meridians and longitudes, knot groups, etc. are, but I don't think there's an explanation of what knot surgery would be and so I'm not sure how Kirby calculus fits into the picture.
Edit: An article by B. Morin on Sikora's dictionary (and how it relates to Lichtenbaum's cohomology, p. 28): "he has given proofs of his results which are very different in the arithmetic and in the topological case. In this paper, we show how to provide a unified approach to the results in the two cases. For this we introduce an equivariant cohomology which satisfies a localization theorem. In particular, we obtain a satisfactory explanation for the coincidences between Sikora's formulas which leads us to clarify and to extend the dictionary of arithmetic topology." 
A: There are some cryptic remarks about this in the first few pages of this talk of Fujiwara:
http://www.ms.u-tokyo.ac.jp/~t-saito/conf/rv/Leopoldt.pdf
(n.b. I believe - though I'm not 100% sure - that some of the later material in these slides has been retracted. But the relevant part is early on.)
A: My post is not an answer, but rather a suggestion of work which belongs to this circle of ideas : Sugiyama gives a geometric analog of the Birch and Swinnerton-Dyer conjecture in http://geoquant.mi.ras.ru/sugiyama.pdf
A: I think it's important to keep track of the fact that the analogy isn't between individual number fields and individual 3-manifolds; it's between the collection of all number fields and the collection of all 3-manifolds.  So in my opinion it's slightly awry to ask for an "arithmetic Poincare conjecture" about Spec Z; I don't think Spec Z should be thought of as analogous to S^3 in any meaningful sense.
As always, John Baez has useful things to say.
I saw Deninger give a beautiful talk about his point of view on this, some of which is recorded in this paper.  Part of the idea, somewhat vaguely, is that you should think of a number field not as an unadorned 3-manifold but as a 3-manifold with a flow on it.  And then the finite primes are not just knots, but closed orbits of that flow!  That gives a more satisfying answer to "why should a 3-manifold have a distinguished countably infinite family of knots on it," makes the connection with dynamical zeta functions, etc.
A: This has been well-addressed by the answerers before me, but just to chime in -- there are a variety of analogs one could make for the Poincare conjecture for number fields.  For one, there are several equivalent statements about the Poincare conjecture for 3-manifolds which are not equivalent when transferred over by analogy to the number field case.  As a first easy example, while 3-manfiolds enjoy a clean Poincare duality, number fields have extra 2-torsion.  In particular, one frequently has $H^1(\mathcal{O}_K,\mathbf{G}_m)$ trivial with $H^2(\mathcal{O}_K,\mathbf{G}_m)$ non-trivial (example: any real quadratic number field with trivial class group).  The equivalences (or lack thereof) between being an integral homology 3-sphere, a rational homology 3-sphere, and a homotopy 3-sphere are not the same in the two "categories."  So depending on how you phrase your analogous Poincare conjecture, you may get different answers.  The cleanest form (found in Niranjan Ramachandran's "A Note on Arithmetic Topology", which deals exclusively with this question) is that there are exactly ten rational homology 3-spheres which are homotopy 3-spheres, namely the 9 quadratic imaginary number fields of class number one and $\mathbb{Q}$ itself.  (Or really, $\mathbb{Z}$ itself), and even more homotopy 3-spheres.
A second frequently under-emphasized point to make is that no one really knows what the right category for this analogy is on the number theory side.  As mentioned above, if you take your category to be Specs of rings of integers in a number field, you don't get the Poincare conjecture.  On the other, if you take the point of view of Artin-Verdier theory (or alternatively, Arakelov theory), where you include in your spaces some information about the behavior of the infinite primes (from the point of view of number theory, defining Spec(Z) as the set of prime ideals ignores the obviously important primes at infinity), then you get a different cohomology theory.  With these new cohomology groups in place, some things look a little bit cleaner.  Again, see Ramachandran.
