Hi Fabian! Kronheimer and Mrowka's book Monopoles and three-manifolds lays out comprehensively the construction of a Seiberg-Witten TQFT, called monopole Floer homology.
It is conjectured to be isomorphic to the Heegaard Floer homology TQFT of Ozsváth-Szabó.
There are also beautiful constructions due to Froyshov and to Manolescu which do not apply in quite so much generality.
The structure of monopole Floer homology is as follows. The TQFT is a functor on the cobordism category $COB_{3+1}$ whose objects are connected, smooth, oriented 3-manifolds. In fact, the TQFT consists of a trio of functors, denoted $\widehat{HM}_{\bullet}$, $\overline{HM_\bullet}$ and $\check{HM}_{\bullet}$ (the last of these is such a sophisticated invariant that you have to download a special LaTeX package just to typeset it properly). These are $\mathbb{Z}[U]$-modules; there's a story about gradings that's too long to be worth summarising here. There are natural transformations which, for any connected 3-manifold $Y$, define the maps in a long exact sequence
$$ \cdots\to \widehat{HM} _{\bullet}(Y) \to \overline{HM_\bullet}(Y)\to \check{HM}_{\bullet}(Y) \to \widehat{HM}_{\bullet}(Y) \to \cdots
$$
Why this structure? Well, the theory is based on the Chern-Simons-Dirac functional $CSD$ on a global Coulomb gauge slice through a space of (connection, spinor) pairs. $CSD$ is a $U(1)$-equivariant functional, and $\check{HM}_{\bullet}$ is, philosophically, its $U(1)$-equivariant semi-infinite Morse homology. $\overline{HM}_\bullet$ is the part coming from the restriction of $CSD$ to the $U(1)$-fixed-points, and $\widehat{HM}_\bullet$ is the equivariant homology relative to the fixed point set.
Now here's a subtlety for the TQFT enthusiasts out there to get your teeth into (axiomatize, explain...)! The invariant of a closed 4-manifold $X$ in any of the three theories is... zero. The famous SW invariant of a 4-manifold with $b_+>0$ comes about via a secondary operation, not part of the TQFT itself. Delete two balls from $X$ to get a cobordism from $S^3$ to itself. When $b_+(X)>0$, there are generically no reducible SW monopoles on this cobordism, and this implies that the TQFT-map $\widehat{HM}_\bullet(S^3) \to \widehat{HM}_\bullet(S^3)$ lifts canonically to a map $\widehat{HM}_\bullet(S^3) \to \check{HM}_\bullet(S^3)$; it is this lift that carries the SW invariant.
There are many surveys and books with open problems, but it would be nice to have a list of a dozen problems that are open and yet embarrasingly simple to state. A list that is "folklore" and that every graduate student in differential geometry should keep in his/her pocket.
Here are the ones I like best:
1. Does every Riemannian metric on the $3$-sphere have infinitely many prime closed geodesics? Does it have at least three (prime) closed geodesics?
2. If the volume of a Riemannian $3$-sphere is equal to 1, does it carry a closed geodesic whose length is less that $10^{24}$? Same question with
$S^1 \times S^2$ if you like it better than the $3$-sphere.
3. Does $S^2 \times S^2$ admit a Riemannian metric with positive sectional curvature?
4. If a Riemannian metric on real projective space has the same volume as the canonical metric, does it carry a closed, non-contractible geodesics whose length is at most $\pi$ ?
5. What are the solutions of the isoperimetric problem in the complex projective plane provided with its canonical (Fubini-Study) metric?
6. Up to constant multiples, is the canonical metric on the complex projective plane the only Riemannian metric on this manifold for which all geodesics are closed?
7. Does every Riemannian metric on the $2$-sphere that is sufficiently close to the canonical metric and whose area is $4\pi$ carry a closed geodesic whose length is at most $2\pi$?
Best Answer
One basic structural problem about the SW invariants is the question of simple type: suppose that $X$ is a simply connected 4-manifold with $b^+>1$, and $\mathfrak{s}$ a $\mathrm{Spin}^c$-structure such that $SW_X(\mathfrak{s})\neq 0$. Must $\mathfrak{s}$ arise from an almost complex structure? This is true when $X$ is symplectic (Taubes in "$SW\Rightarrow Gr$") but open in general.
The 11/8-conjecture (that for a closed Spin 4-manifold $X$ of signature $\sigma$, one has $b_2(X)\geq 11|\sigma|/8$) is open. SW theory has yielded strong results in this direction (Furuta's 10/8 theorem); proving the conjecture via SW theory is very hard but might be possible.
Essentially all of the fundamental questions about the classification of smooth 4-manifolds, or about the existence and uniqueness of symplectic structures on them, are open. We do not know how much Seiberg-Witten theory sees. For instance:
Suppose $X$ is a closed 4-manifold with an almost complex structure $J$. Let $w\in H^2(X;\mathbb{R})$ be a class with $w^2>0$. Is there a symplectic form $\omega$ with compatible almost complex structure homotopic to $J$ and symplectic class $w$? The "Taubes constraints" are the following necessary conditions, which constrain the SW invariants in terms of $w$ and $c=c_1(TX,J)$ (see e.g. Donaldson's survey on the SW equations): (i) $SW(\mathfrak{s}_{can})=\pm 1$ (the sign can be made precise) where $\mathfrak{s}_{can}$ is the $\mathrm{Spin}^c$-structure arising from $J$; (ii) $-c\cdot w\geq 0$; and (iii) if $SW(\mathfrak{s})\neq 0$ then $|c_1(\mathfrak{s})\cdot [\omega]| \leq -c \cdot [\omega]$, with equality iff $\mathfrak{s}$ is isomorphic to $\mathfrak{s}_{can}$ or its conjugate. The question is: if $X$ is simply connected, are these sufficient conditions? (Example: Fintushel-Stern knot surgery on an elliptically fibered K3 surface along a knot with monic Alexander polynomial.)