There are a few things going on here.
First, strictly speaking, I don't think GAGA applies here, since $S_1$ is not finite type (e.g. here).
But your interpretation of the roles of $(t)$ and $(0)$ are correct in the case we are studying a degeneration of a family of curves over a DVR. In this case, the family $X\to S_1$ is determined by a homomorphism $\mathbb C[[t]]\to\Gamma(X,\mathcal O_X)$, and there are two fibres to consider: the fibre over the closed point $(t),$ and the fibre over the generic point $(0).$ Over the closed point we will get an honest curve over $\mathbb C,$ while over the generic point, we get a "family" which is just a curve over $\mathbb C((t)).$
What Qiaochu mentions in his answer is actually an arc of the curve $V(f)\in\mathbb C^2.$ You should actually think of this as an infinitesimal analytic approximation of $V(f)$ at $(x(0),y(0)),$ rather than as a family of curves degenerating to $V(f).$
Edit
Let us consider a particular example, just for the sake of having something concrete to look at. We can see what happens if $X$ is something relatively easy, like $\operatorname{Spec}(\mathbb C[[t]][x])=\mathbb A^1_{\mathbb C[[t]]}.$ The morphism $X\to S_1$ is determined by its dual $\mathbb C[[t]]\hookrightarrow\mathbb C[[t]][x].$ Let's check the fibres.
Over $(t)\subseteq\mathbb C[[t]]$ we get $\kappa((t))=\mathbb C$ for the residue field, so the fibre is the spectrum of $\mathbb C[[t]][x]\otimes_{\mathbb C[[t]]}\mathbb C\cong\mathbb C[x].$ Thus, the fibre over $(t)$ is $\mathbb A^1_{\mathbb C},$ which is an honest curve over $\mathbb C.$ Analytically, we think of this as exactly the fibre over $0,$ since $t$ vanishes at $0\in\mathbb C.$
Over $(0)\subseteq\mathbb C[[t]]$ we get $\kappa((0))=\mathbb C((t)),$ and we can compute easily that the fibre is $\mathbb A^1_{\mathbb C((t))},$ which is now a curve over a transcendental field extension of $\mathbb C.$ The fact that this is the fibre over the generic point tells us to consider this curve as being a general member of the "family of curves" $X$, in exactly the same way as the generic point of $\mathbb C[[t]]$ is considered to be a general point in the "infinitesimal neighbourhood" of the origin represented by $S_1$, while the closed point $(t)\subseteq\mathbb C[[t]]$ refers to exactly the origin.
In order to really make a tight connection with the complex analysis picture, I think one has to consider the family $X\to S_1$ as a deformation of the closed fibre over the ring $\mathbb C[[t]].$ In general, once we have a small deformation of an object, the question of deformation theory is whether we can extend the deformation to larger (than $\mathbb C[[t]]$ in this case) base rings, eventually finding the "algebraic" deformations (i.e., over non-local rings) of the given object. As long as certain obstructions vanish, we will be able to compute extensions, though there is a huge theory behind this, and even showing that obstructions vanish can be tough. But, if we have found an algebraic deformation, over something like $\mathbb C[t],$ then we can really use GAGA, or simply the fact that $\mathbb A^1_{\mathbb C}$ is naturally a complex manifold, to find the right correspondence.