Inspired by the discussion in @DaftWullie's answer above, note that we can construct a lattice/Hasse diagram of all classes of Boolean functions realizable/synthesizable with various gate sets. Such a lattice will indicate whether a given gate set is universal for the given class.
For classical (not necessarily reversible) computation, Emil Post did this in the 40's. Thus we have, for example, the well-known results that the [0, 1, ∧, ∨] are only able to synthesize "monotone" functions.
Apparently the same question went mostly unasked throughout most of the history of reversible computation; nonetheless, not too long ago Aaronson, Grier, and Schaeffer were able to build such a lattice. Their full classification allows for ancillas, and clocks in at 68 pages, but their Theorem 3 separates the class of functions realizable with CNOTs from those realizable with Toffoli gates.
Briefly and from a quick perusal of the above paper, CNOT gates (even with extra ancillas) are affine over $\mathbb{F}_2$, while CCNOT gates (Toffoli gates) are not. Thus CNOT gates alone cannot synthesize non-affine functions, while Toffoli gates can.
Being affine means that, for a circuit $G$ (including ancillas initialized arbitrarily to $0$ or $1$ if necessary), then there exists an invertible matrix $A\in\mathbb{F}_2^{k\times k}$ and a vector $b$ such that $G(x)=Ax\otimes b$ for all $x$.