I am trying to recount which 'space' structures are defined by a collection of subsets. Given a set $X$ the only two structures I know are:
(1) $\mathcal{T}\subseteq \mathcal{P}(X)$ is a topology on $X$, and $(X,\mathcal{T})$ is a topological space.
(2) $\mathcal{F}\subseteq \mathcal{P}(X)$ is a $\sigma$-algebra on $X$, and $(X,\mathcal{F})$ is a measurable space.
Are there any more such famous structures given by a collection of subsets?
In measure theory there are often technical such structures (semi-algebra/algebra on a set $X$, $\pi$-system, $\lambda$-system) that are used in the development of the theory, but are rarely studied independently, so I'll ignore them...
A bornological space ("bounded sets") is another one occurring in analysis.
A more geometric one is abstract convexity structures (where we have an axiomatisation of convex sets, but there are also metric convexities, order convexities etc. see the standard reference book by van de Vel for much more info. These are closed under arbitary intersections, contain $\emptyset$ and $X$, and are closed under all up-directed unions, to summarise the axioms. It's very much in the spirit of topology (separation axioms etc.), IMHO it's a nice theory that deserves more attention.
Stretching it a bit, (undirected) graphs are sets with special "doubleton sets" (the edges), but these have no special axioms. One can generalise to multigraphs and incidence structures and matroids (the "independent" subsets). The last one are a proper example in your sense, I think.
Maybe others can come up with more than bornological spaces, convexity structures and matroids.