Consider the graphs of the functions $f_1(x) = |x|$, and $f_2(x) = x$ under the subspace topology of $\mathbb{R}^2$.
Both of these graphs are smooth manifolds, just pick coordinate charts to be $(x, f_i(x)) \leftrightarrow x$.
Moreover, they are diffeomorphic via the map $(x, f_1(x)) \rightarrow (x, f_2(x))$.
This seems to clash with my intuition. For example, the graph of $f_1$ has a corner, so it "shouldn't" be smooth, much less diffeomorphic to $f_2$, which is just a straight line.
Can someone explain what's going on here?
In light of these examples, how should I visualize smooth manifolds and diffeomorphisms?
Your intuition is broken because the inclusion of the graph of $f_1$ (with the smooth structure you describe) into $\mathbb{R}^2$ isn't smooth. The graph of $f_1$, as a subset of $\mathbb{R}^2$ with its usual smooth structure, is not a smooth manifold for exactly the intuitive reason.