Let $G$ be a group acting on a set $X$. Burnside's Lemma says that
$$
|X/G| \;=\; \frac{1}{|G|} \sum_{g\in G} |X^g|,
$$
where $X/G$ is the set of orbits in $X$ under $G$, and $X^g$ denotes the set of elements of $X$ fixed by the element $g$. This lemma follows fairly immediately from the Orbit-Stabilizer Theorem (see the short proof in the Wikipedia article).
Using Burnside's lemma, it is not too hard to count the isomorphism classes of graphs with $n$ vertices. Let $E$ be the set of $\binom{n}{2}$ edges of a complete graph with $n$ vertices. Then any graph $\Gamma$ with $n$ vertices corresponds to a subset of $E$, i.e. a function $f_\Gamma\colon E\to \{0,1\}$.
Given any permutation $\sigma \in S_n$ of the $n$ vertices, let $\sigma_E$ be the corresponding permutation of the elements of $E$. Then a graph $\Gamma$ is stabilized by $\sigma$ if and only if $f_\Gamma$ is constant on the edges of each cycle of $\sigma_E$. Thus, the number of graphs stabilized by $\Gamma$ is $2^{N(\sigma_E)}$, where $N(\sigma_E)$ denotes the number of cycles in $\sigma_E$. By Burnside's Lemma, it follows that the number of isomorphism classes is
$$
\frac{1}{|S_n|}\sum_{\sigma\in S_n} 2^{N(\sigma_E)}
$$
Example: Let's compute the number of graphs with four vertices. The group $S_4$ has five different types of elements:
- The identity element,
- Six two-cycles,
- Eight three-cycles,
- Six four-cycles, and
- Three elements of the form $(*\;\;*)(*\;\;*)$
Obviously $N(\sigma_E) = |E| = 6$ if $\sigma$ is the identity element. If $\sigma=(1\;2)$, then $\sigma_E$ has four cycles:
$$
\sigma_E \;=\; \bigl(\{1,2\}\bigr)\;\bigl(\{1,3\}\;\;\{2,3\}\bigr)\;\bigl(\{1,4\}\;\;\{2,4\}\bigr)\;\bigl(\{3,4\}\bigr).
$$
If $\sigma = (1\;2\;3)$, then $\sigma_E$ has two cycles:
$$
\sigma_E \;=\; \bigl(\{1,2\}\;\;\{2,3\}\;\;\{1,3\}\bigr)\;\bigl(\{1,4\}\;\;\{2,4\}\;\;\{3,4\}\bigr).
$$
If $\sigma = (1\;2\;3\;4)$, then $\sigma_E$ has two cycles:
$$
\sigma_E \;=\; \bigl(\{1,2\}\;\;\{2,3\}\;\;\{3,4\}\;\;\{1,4\}\bigr)\;\bigl(\{1,3\}\;\;\{2,4\}\bigr).
$$
Finally, if $\sigma=(1\;2)(3\;4)$, then $\sigma_E$ has four cycles:
$$
\sigma_E \;=\; \bigl(\{1,2\}\bigr)\;\bigl(\{3,4\}\bigr)\;\bigl(\{1,3\}\;\;\{2,4\}\bigr)\;\bigl(\{1,4\}\;\;\{2,3\}\bigr).
$$
Thus, the number of isomorphism classes of graphs with $4$ vertices is
$$
\frac{1}{|S_n|}\sum_{\sigma\in S_n} 2^{N(\sigma_E)} \;=\; \frac{2^6 + 6(2^4) + 8(2^2) + 6(2^2)+3(2^4)}{24} \;=\; 11.
$$
Wikipedia has a nice picture of these eleven classes:

Improvement: Actually, it's not too hard to find a general formula for $N(\sigma_E)$. In particular:
Each $k$-cycle of $\sigma$ gives rise to $\lfloor k/2\rfloor$ orbits of edges between vertices of the $k$-cycle, and
Each $\{j$-cycle, $k$-cycle$\}$ pair gives rise to $\gcd(j,k)$ orbits of edges between vertices in the two cycles.
Thus, if $\sigma$ has cycles of length $k_1,\ldots,k_m$ (including cycles of length $1$), then
$$
N(\sigma_E) \;=\; \sum_{i=1}^m \left\lfloor\frac{k_i}{2}\right\rfloor \,+\, \sum_{i<j} \gcd(k_i,k_j).
$$
For example, if $\sigma$ is the product of $6$-cycle, a $4$-cycle, and a $1$-cycle, then
$$
N(\sigma_E) \;=\; \left\lfloor\frac{6}{2}\right\rfloor + \left\lfloor\frac{4}{2}\right\rfloor + \left\lfloor\frac{1}{2}\right\rfloor + \gcd(6,4) + \gcd(6,1) + \gcd(4,1) \;=\; 9.
$$
Example: Let's compute the number of isomorphim classes of graphs with $5$ vertices. Here are the possible cycle structures for elements of $S_5$:
- $\sigma=(*)(*)(*)(*)(*)$, $1$ element, $N(\sigma_E) = 10$
- $\sigma=(*\;*)(*)(*)(*)$, $10$ elements, $N(\sigma_E) = 7$
- $\sigma=(*\;*\;*)(*)(*)$, $20$ elements, $N(\sigma_E) = 4$
- $\sigma=(*\;*\;*\;*)(*)$, $30$ elements, $N(\sigma_E) = 3$
- $\sigma = (*\;*\;*\;*\;*)$, $24$ elements, $N(\sigma_E) = 2$
- $\sigma = (*\;*)(*\;*)(*)$, $15$ elements, $N(\sigma_E) = 6$
- $\sigma = (*\;*\;*)(*\;*)$, $20$ elements, $N(\sigma_E) = 3$
Thus, the number of isomorphism types of graphs with five vertices is:
$$
\frac{1(2^{10}) + 10(2^7) + 20(2^4) + 30(2^3) + 24(2^2) + 15(2^6) + 20(2^3)}{120} \;=\; 34.
$$