A couple very disparate answers that spring to mind (fortunately, this is community wiki, and actual experts should feel very free to improve my exposition of either):
The negative gradient flow for the Chern-Simons functional on a 3-manifold $M$ naturally satisfies a four-dimensional symmetry. Namely, if one has a principal $G$-bundle on $M$ and some connection $A$ on this $G$-bundle (which I'll carelessly think of as a $\mathfrak{g}$-valued $1$-form on $M$), the Chern-Simons functional $CS(A) = \int_M \Big( dA + \frac{2}{3} A \wedge A \Big) \wedge A$ is a perfectly well-defined function on the space of connections, and one can attempt to perform the negative gradient flow with respect to a natural metric on this space of connections (this being a very natural thing to do from the point of view of Morse theory, for example). If you want, you can interpret the solution to this flow as a connection on the bundle pulled back to $M \times \mathbb{R}$, and while this connection clearly transforms nicely under $Diff(M)$, there's no particular reason to think it's a well-behaved object under the diffeomorphism group of the four-manifold $M \times \mathbb{R}$. However, this negative gradient flow equation turns out to be exactly the anti-self dual equation $F^+ = 0$, where the curvature $F = dA + A \wedge A$ and its self-dual part is $F^+ = \frac{1}{2}(F + *F)$. This equation manifestly respects the symmetries of the entire four-manifold, and this point of view is a very effective one for proving even basic things, like gauge invariance, of the Chern-Simons functional. Witten is very fond of making this point and my understanding is that this insight allowed him to extend his QFT description of the Jones polynomial to a QFT description of its categorification, Khovanov homology.
And now for something completely different: associativity of the quantum cup product. A familiar object to many people is the cohomology ring $H^*(X)$ of a space $X$, which is associative, (graded) commutative, and just generally great. If $X$ is a symplectic manifold, there's an interesting way to deform the multiplication on this ring using counts of $J$-holomorphic curves passing through various cycles. In effect, one picks a compatible almost-complex structure on the symplectic manifold, and then if one writes $\alpha * \beta = \sum_{\gamma} c_{\alpha \beta \gamma} \gamma$, where we think of $\alpha, \beta, \gamma$ as cycles in $X$ (using Poincare duality), the coefficient $c_{\alpha \beta \gamma}$ is a generating function in some formal variables, the coefficients of which are counts of holomorphic curves of fixed genus and homology class intersecting our three cycles $\alpha, \beta, \gamma$. Using this deformed multiplication gives the quantum cohomology ring $QH^*(X)$. Now, some properties of this ring, like graded commutativity, are fairly easy to see from the definition, but associativity is really quite tricky! (I realise this isn't exactly what you asked in your question as it's not just a symmetry of some coefficient, but you can phrase associativity as a symmetry of something or other -- if you want to be technical, a four-point Gromov-Witten invariant -- so I think it qualifies.) The associativity is somehow not so bad to see in the algebro-geometric case (or perhaps this is just my bias as an algebraic geometer), but in symplectic geometry you really need some nontrivial analytic estimates at some point in the proof. And you get a lot out of it! Associativity of this quantum cohomology ring encapsulates a wealth of information on enumerative geometry counts associated to $M$; indeed, it was basically this idea that allowed Kontsevich to find his recursion for the number of degree $d$ curves through $3d + 1$ general points in $\mathbb{P}^2$.
Finally, I kind of want to mention strange duality, even though that now really isn't an answer to the question, as you have to modify one side or the other; I'll just copy a very quick summary from the abstract to arxiv.org/abs/math/0602018: ``For X a compact Riemann surface of positive genus, the strange duality conjecture predicts that the space of sections of certain theta bundle on moduli of bundles of rank r and level k is naturally dual to a similar space of sections of rank k and level r.'' The paper itself is a great place to learn more about it if you're interested!