Find a recursive formula for the following example. The number of binary strings of length $n$, such that there are no $3$ consecutive $0's$.
I started by considering the length $n$ as a block ($1$ row) with $n$ many columns. I started off by considering only the last column, marked $x$. Here's my working:
Int the case that the very last string is $0$, I think my working out is correct. Now, if the last string is $1$, then I'm left with $n-1$ without any further complications. Therefore, $a_n= 2a_{(n-1)}+a_{(n-2)}+a_{(n-3)}$. Is this correct?

Critique
The diagram in the question is correct, but the recursion drawn from it is slightly off. In the diagram, it is shown that each of the $a_n$ strings of length $n$ with out a '$000$' can be classified as follows:
It ends in a '$\boldsymbol{1}$':$\phantom{00}$ $\overbrace{\boxed{\phantom{0\times\times\times\times000\times}}\boxed{\times\vphantom{0}}}^{n-1}\!\,\boxed{1\vphantom{\times}}$ There are $a_{n-1}$ of these.
It ends in a '$\boldsymbol{10}$':$\phantom{0}$ $\overbrace{\boxed{\phantom{0\times\times00\times\times}}\boxed{\times\vphantom{0}}}^{n-2}\!\,\boxed{1\vphantom{\times}}\boxed{0\vphantom{\times}}$ There are $a_{n-2}$ of these.
It ends in a '$\boldsymbol{100}$': $\overbrace{\boxed{\phantom{0\times\times\times\times}}\boxed{\times\vphantom{0}}}^{n-3}\!\,\boxed{1\vphantom{\times}}\boxed{0\vphantom{\times}}\boxed{0\vphantom{\times}}$ There are $a_{n-3}$ of these.
Therefore, adding these cases up, we get $$ a_n=a_{n-1}+a_{n-2}+a_{n-3}\tag1 $$ In the question, it seems that the intermediate tree node, i.e. $\overbrace{\boxed{\phantom{0\times\times\times\times}}\boxed{\times\vphantom{0}}}^{n-1}\!\boxed{0\vphantom{\times}}$, is being included in the counting, but that node is counted in the leaves below it.
Generating Function Approach
Let $x$ represent the atom '$1$', $x^2$ represent the atom '$10$', and $x^3$ represent the atom '$100$'.
$\left(x+x^2+x^3\right)^k$ counts the strings made up of $k$ atoms; the coefficient of $x^n$ telling the how many strings of length $n$ can be made from $k$ atoms. After adding up the contributions from all numbers of the atoms, we handle the strings starting with '$0$' and '$00$' by multiplying by $\left(1+x+x^2\right)$ to get the generating function for the number of strings that can be made up from any number of atoms is $$ \begin{align} \left(1+x+x^2\right)\sum_{k=0}^\infty\left(x+x^2+x^3\right)^k &=\left(1+x+x^2\right)\sum_{k=0}^\infty\left(\frac{x-x^4}{1-x}\right)^k\\ &=\left(1+x+x^2\right)\frac1{1-\frac{x-x^4}{1-x}}\\ &=\left(1+x+x^2\right)\frac{1-x}{1-2x+x^4}\\[3pt] &=\frac{1+x+x^2}{1-x-x^2-x^3}\\[9pt] &=1+2x+4x^2+7x^3+13x^4+24x^5+\dots \end{align} $$ The denominator of $1-x-x^2-x^3$ gives the recurrence $a_n=a_{n-1}+a_{n-2}+a_{n-3}$.