There is one point that is mentioned in passing in Moishe Cohen's nice answer that deserves a bit of elaboration, which is that a lot of the time it is not important for a manifold to have a countable basis. Rather, what is important in most applications is for a manifold to be paracompact: this is what gives you partitions of unity, which are essential to an enormous amount of the theory of manifolds (for instance, as the other answer mentioned, proving that any manifold admits a Riemannian metric).
Paracompactness follows from second-countability, which is the main reason why second-countability is useful. Paracompactness is weaker than second-countability (for instance, an uncountable discrete space is paracompact), but it turns out that it isn't weaker by much: a (Hausdorff) manifold is paracompact iff each of its connected components is second-countable. To put it another way, a general paracompact manifold is just a disjoint union of (possibly uncountably many) second-countable manifolds. So if you care mainly about connected manifolds (or even just manifolds with only countably many connected components), you lose no important generality by assuming second-countability rather than paracompactness.
There are also a few situations where it really is convenient to assume second-countability and not just paracompactness. For instance, in the theory of Lie groups, it is convenient to be able to define a (not necessarily closed) Lie subgroup of a Lie group $G$ as a Lie group $H$ together with a smooth injective homomorphism $H\to G$. If you allowed your Lie groups to not be second-countable, you would have the awkward and unwanted example that $\mathbb{R}$ as a discrete space is a Lie subgroup of $\mathbb{R}$ with the usual $1$-dimensional smooth structure (via the identity map). For instance, this example violates the theorem (true if you require second-countability) that a subgroup whose image is closed is actually an embedded submanifold.