$S^2$ is 2-dim sphere , $T^2$ is 2-dim torus. $L^2$ is Lebesgue spaces. What is the difference of $L^2(S^2)$ and $L^2(T^2)$ ?
In fact, I don't know how to define the difference ,because isomorphism of Hilbert space can't distinguish them. But I feel there should be some difference.
This is a loose question, I am sorry for this , but I really don't know how to ask it exactly.
This doesn't apply to Hilbert spaces, but you might be interested in the fact that if you shift your attention to Banach algebras you have the Gelfand Representation, which I think of as a way to go from a function/operator space back to the underlying topological space. I think this addresses the underlying spirit of your 'loose' question.
If that scratches your itch, you could look into Noncommutative Geometry, which takes the ideas further.