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One obtains the compact Hausdorff space $X$ (up to homeomorphism) from $C(X)$ by considering the maximal ideal space of $C(X)$ with Gelfand topology, but clearly you want something less tautological than "the maximal ideal space is a manifold." A small step in this direction would be to try to formulate the topological properties of $X$ in terms of the closed ideals of $C(X)$. As alluded to in Qiaochu's comment, there is an analogue of Nullstellensatz: each closed ideal in $C(X)$ consists of all functions vanishing on a (uniquely determined) closed subset of $X$. So for example, the locally Euclidean property could be reformulated for a commutative C*-algebra $A$ as follows: There is an $n$ such that for every maximal ideal $M$ of $A$ there is a closed ideal $I$ of $A$ such that $I$ is not contained in $M$ and $I$ is $*$-isomorphic to $C_0(\mathbb{R}^n)$. Second countability of the maximal ideal space is equivalent to $A$ being separable in the norm topology; that's not algebraic, but might be considered more intrinsic to the C*-algebra.
But this only leads to another, more specific question: Is there a useful or interesting (C*-)algebraic characterization of $C_0(\mathbb{R}^n)$?
Browder proved a theorem relating the number of generators of a complex commutative Banach algebra to the Čech cohomology with complex coefficients of the maximal ideal space, and as a corollary concluded that if $M$ is a compact orientable $n$-dimensional manifold, then $C(M)$ cannot be generated as a Banach algebra by fewer than $n+1$ elements. The paper is very short, but for an even shorter summary here's the MR review.