How are $\sigma$ and $\sigma^\pm$ determined in Hammett plots?
Hammett wanted to find a way to quantify the effects electron-withdrawing (EWG) and - donating (EDG) groups have on the transition state or intermediate during the course of a reaction. Initially he took the $pK_{\mathrm{a}}$-values of benzoic acids carrying the respective functional group in para or meta position (ortho acids and aliphatic acids weren't used because steric effects would overlay with the electronic effects) as a guide and plotted them against the logarithm of the reaction rates.
So, he based his scale on the following reaction reaction:



Later Hammett decided not to use the $pK_{\mathrm{a}}$s themselves for his correlation but defined a new parameter, which he called $\sigma$.
This $\sigma$ shows how electron-donating or -withdrawing a group is relative to $\ce{H}$ as a ratio of
the $\log K_a$s or the difference of the $pK_{\mathrm{a}}$
between the substituted benzoate and benzoic acid itself.
If the acid required to determine $\sigma$ for a new substituent was not available, $\sigma$ could be determined by correlation with other reactions.
A different value of $\sigma$ for any given substituent was needed for the meta and para positions (sometimes called $\sigma_{\mathrm{m}}$ and $\sigma_{\mathrm{p}}$, respectively). 
The equation for $\sigma$ is

\begin{equation}
\sigma_{\ce{X}} = \log \left( \frac{ K_{\mathrm{a}}(\ce{X-C6H4COOH}) }{ K_{\mathrm{a}}(\ce{H-C6H4COOH}) } \right) = pK_{\mathrm{a}}(\ce{X-C6H4COOH}) - pK_{\mathrm{a}}(\ce{H-C6H4COOH})
\end{equation}

or in short notation

\begin{equation}
\sigma_{\ce{X}} = \log \left( \frac{ K_{a} (\ce{X}) }{ K_{a} (\ce{H}) } \right) = pK_{\mathrm{a}}(\ce{X}) - pK_{\mathrm{a}}(\ce{H})
\end{equation}

where $\ce{X}$ is the functional group, i.e. the EWG or EDG, whose effect on the reaction rate shall be evaluated.
It is also possible to determine the $\sigma$ values via the logarithm of the ratio of the rate constants for the aforementioned reaction with substituent $\ce{X}$ (in short notation: $k_{\ce{X}}$) and with $\ce{X}=\ce{H}$ (in short notation: $k_{\ce{H}}$)

\begin{equation}
\sigma_{\ce{X}} = \log \left( \frac{ k_{\ce{X}} }{ k_{\ce{H}} } \right)
\end{equation}

Update

AcidFlask's comment reminded me that I forgot to say something about $\sigma^{+}$ and $\sigma^{-}$ values.
As mentioned above the "normal" $\sigma$ values are based upon the difference of the $pK_{\mathrm{a}}$ between a substituted benzoate and benzoic acid itself.
But for benzoates one cannot draw resonance structures that delocalize the negative charge onto the benzene ring via the $\pi$ electron system.
Yet, many reations of interest create negative or positive charges that can be stabilized by delocalization via resonance with the substituent.
For these reactions, one finds that Hammett plots using $\sigma$ values have considerable scatter.
Therefore, two new substituent effect scales were produced, one for groups that stabilize negative charges via resonance ($\sigma^{-}$), and one for groups that stabilized positive charges via resonance ($\sigma^{+}$).
The $\sigma^{-}$ scale is based upon the ionization of para-substituted phenols (I've found different accounts for this. According to the German Wikipedia the $\sigma^{-}$ scale is based upon the ionization of para-substituted anilins.),



for which groups like nitro can stabilize the negative charge via resonance.
The $\sigma^{+}$ scale is based upon the heterolysis ($\mathrm{S}_{\mathrm{N}}1$) reaction of para-substituted cumyl chlorides (phenyldimethyl chloromethanes),



for which groups like amino can stabilize the positive charge via resonance.
The $\sigma^{\pm}$ values can then be evaluated by the aforementioned equation

\begin{equation}
\sigma_{\ce{X}}^{\pm} = \log \left( \frac{ K_{a}^{\pm} (\ce{X}) }{ K_{a}^{\pm} (\ce{H}) } \right) = \log \left( \frac{ k_{\ce{X}}^{\pm} }{ k_{\ce{H}}^{\pm} } \right)
\end{equation}

but with the rate constants $k_{\ce{X}}^{\pm}$ and $k_{\ce{H}}^{\pm}$ (or the equilibrium constants $K_{a}^{\pm} (\ce{X})$ and $K_{a}^{\pm} (\ce{H})$) measured for their respective defining reactions.