As already answered by SAUVIK, if $f:E\longrightarrow F$,
$$Df(x)\in L(E,F)\text{ and } Df:E\longrightarrow L(E,F).$$
So,
$$D^2 f:E\longrightarrow L(E,L(E,F)).$$
Now, the space $L(E,L(E,F))$ can be identified of the space of bilinear functions form $E$ to $F$ via the isomorphism
$$g\to\hat g,\qquad\hat g(x,y) = (g(x))(y).$$
The trick can be obviously extended to higher orders.
To understand it, you have to treat derivatives as linear operators. If $f:\mathbb{R}^n\to\mathbb{R}^m$ then $$f':\mathbb{R}^n\to L(\mathbb{R}^n,\mathbb{R}^m)$$
where $ L(\mathbb{R}^n,\mathbb{R}^m)$ is the set of linear transformations from $\mathbb{R}^n$ to $\mathbb{R}^m$. It can be identified with $M_{n\times m}$ or $\mathbb{R}^n\times \mathbb{R}^m$. If you identify it with $\mathbb{R}^{n+m}$ you see that differentiate the matrix is the same as differentiate the function $f':\mathbb{R}^n\to\mathbb{R}^{n+m}$ and the last you know how to differentiate. Moreover, because $f'(x)$ is a linear transformation for all $x$, you have to understand how this transformation works and it works according with the formula $$f'(x)u=A_x u$$
where $A_x$ is the matrix of derivatives which is in your question.
To proceed we have that $$f'':\mathbb{R}^n\to L(\mathbb{R}^n, L(\mathbb{R}^n,\mathbb{R}^m))$$
Now $f''$ is a function which send $x$ to a linear transformation $f''(x)$ from $\mathbb{R}^n$ to $ L(\mathbb{R}^n,\mathbb{R}^m)$. But such linear operator can be identified with a bilinear form $g(x)$ by considering $g(x):\mathbb{R}^n\times \mathbb{R}^n\to\mathbb{R}^m$ defined by $$g(x)uv=f''(x)uv$$
Moreover, note that $$f''(x)uv=[f'(x)u]'v$$
hence $f''(x)$ is the bilinear form defined by $$f''(x)uv=[A_xu]'v$$
where $$[A_xu]'=\left( \begin{array}{ccc}
\frac{\partial \sum_{i=1}^n\frac{\partial f_1}{\partial x_i}u_i}{\partial x_1} & ... & \frac{\partial \sum_{i=1}^n\frac{\partial f_1}{\partial x_i}u_i}{\partial x_n} \\
... & ... & ... \\
\frac{\partial \sum_{i=1}^n\frac{\partial f_m}{\partial x_i}u_i}{\partial x_1} & ... &\frac{\partial \sum_{i=1}^n\frac{\partial f_m}{\partial x_i}u_i}{\partial x_n} \end{array} \right)$$
For example, consider the function $f(x,y)=(x^2-y,x+y^2)$. We can identify $$f'(x,y)= \left( \begin{array}{cc}
2x & -1 \\
1 & 2y \end{array} \right) = (2x,1,-1,2y)$$
and we know that $$f'(x,y)(u,v)=\left( \begin{array}{cc}
2x & -1 \\
1 & 2y \end{array} \right)\left( \begin{array}{c}
u \\
v \end{array} \right)$$
Now, $f''(x,y)(u,v)(z,w)=[f'(x,y)(u,v)]'(z,w)$, but $$f'(x,y)(u,v)=(2xu-v,u+2yv)$$
Now we think on $(u,v)$ in the last expression as constants and $$f''(x,y)(u,v)=\left( \begin{array}{cc}
2u & 0 \\
0 & 2v \end{array} \right)$$
which implies that $$f''(x,y)(u,v)(z,w)=(2uz,2vw)$$
The case $f^{(n)}$ is similar.
Best Answer
The Jacobian matrix is the best linear approximation to $f$ at a particular point. However, if you change the point, you get a different Jacobian. The second derivative quantifies how the Jacobian changes as the point of approximation changes - the "change of the change".
To that end, we can think of the derivative $D$ as a mapping from the domain of the original function to the space of linear maps $\mathcal{L}(X,Y)$ with domain $X$ and range $Y$ the same as the original function: \begin{align} f:& X \rightarrow Y \\ Df:& X \rightarrow \mathcal{L}(X,Y) \end{align} The derivative of $f$, $Df$, is a function where you put in a point and it gives you a linear function, $$Df(x_0) = \text{best linear function approximating $f$ near }x_0.$$
In matrix form, $Df(x_0)$ is the Jacobian matrix $J$ at $x_0$: $Df(x_0)(y) = J|_{x_0} y$.
Since $Df$ is itself a function, we can take it's derivative, and so on, getting a tower of higher and higher derivatives as follows:
\begin{align} f:&\mathbb{R}^n \rightarrow \mathbb{R}^m \\ Df:&\mathbb{R}^n \rightarrow \mathcal{L}(\mathbb{R}^n, \mathbb{R}^m) \\ D(Df) = D^2f:&\mathbb{R}^n \rightarrow \mathcal{L}(\mathbb{R}^n, \mathcal{L}(\mathbb{R}^n, \mathbb{R}^m)) \\ D(D^2f) = D^3f:&\mathbb{R}^n \rightarrow \mathcal{L}(\mathbb{R}^n,\mathcal{L}(\mathbb{R}^n, \mathcal{L}(\mathbb{R}^n, \mathbb{R}^m))) \\ \dots \end{align}
Now this gets confusing fast (spaces of linear maps mapping to spaces of linear maps mapping to... ack!!). Luckily there is an isometric isomorphism theorem saying that everything just boils down to multilinear maps: $$\mathcal{L}^n(X,\mathcal{L}^m(X,Y)) \cong \mathcal{L}^{n+m}(X,Y),$$ where $\mathcal{L}^k(X,Y)$ is the space of $k$-linear maps from $X$ to $Y$, and $\cong$ denotes an isometric isomorphism of function spaces. In more detail, what it means for $g$ to be in $\mathcal{L}^k(X,Y)$ is that $g : X \times \dots \times X \rightarrow Y$, and $g$ is independently linear in each of it's entries: $$g(x_a + x_b,z,w) = g(x_a,z,w) + g(x_b,z,w),$$ $$g(x,y_a+y_b,w) = g(x,y_a,w) + g(x,y_b,w),$$ and so on.
So, now we can simplify our tower of derivatives using spaces of multilinear functions: \begin{align} f:&\mathbb{R}^n \rightarrow \mathbb{R}^m \\ Df:&\mathbb{R}^n \rightarrow \mathcal{L}(\mathbb{R}^n, \mathbb{R}^m) \\ D^2f:&\mathbb{R}^n \rightarrow \mathcal{L}^2(\mathbb{R}^n, \mathbb{R}^m) \\ D^3f:&\mathbb{R}^n \rightarrow \mathcal{L}^3(\mathbb{R}^n, \mathbb{R}^m) \\ \dots \end{align}
So, from this picture it is pretty clear what the second derivative of your function $f:X \rightarrow Y$ is at a point. It is a bilinear map from $X \times X$ to $Y$. You put in two vectors from $X$, and it gives out a vector in $Y$, and does so in a way that is linear in each input independently.
If you have a basis $\{ b_i\}$ of $n$ vectors for $X$ and basis $\{e_i\}$ of $m$ vectors for $Y$, you could completely characterize the second derivative by a 3D $n$-by-$n$-by-$m$ array of numbers $T_{ijk}$ where the $(i,j,k)$'th entry is found by applying the bilinear function with $b_i$ in the first argument and $b_j$ in the second argument, and then taking the component of the vector you get out in the $e_k$ direction: $$T_{ijk} = e_k^T D^2f(x_0)(b_i,b_j).$$