For complex drawings (circles, etc), you might need to go the tikz road.
But for simple shading of elements, a regular \colorbox should do, i.e.
\documentclass{article}
\usepackage{xcolor}
\newcommand{\highlight}[1]{%
\colorbox{red!50}{$\displaystyle#1$}}
\begin{document}
\begin{equation}
\mathbf{Y_{ij}} = \highlight{\beta_{0}} +\mathbf{ b_i} + \beta_1x_1 + \ldots + \beta_nx_n + \mathbf{\epsilon_{ij}}
\end{equation}
\end{document}
which yields

In case you want to do more than just highlight terms but are looking to explain the terms, I once wrote the following code for my master's thesis presentation:
\documentclass{article}
\usepackage{xcolor}
\newlength{\overwritelength}
\newlength{\minimumoverwritelength}
\setlength{\minimumoverwritelength}{1cm}
\newcommand{\overwrite}[3][red]{%
\settowidth{\overwritelength}{$#2$}%
\ifdim\overwritelength<\minimumoverwritelength%
\setlength{\overwritelength}{\minimumoverwritelength}\fi%
\stackrel
{%
\begin{minipage}{\overwritelength}%
\color{#1}\centering\small #3\\%
\rule{1pt}{9pt}%
\end{minipage}}
{\colorbox{#1!50}{\color{black}$\displaystyle#2$}}}
\begin{document}
\begin{equation}
\mathbf{Y_{ij}} = \overwrite{\beta_{0}}{very important!} +\mathbf{b_i} + \beta_1x_1 + \ldots + \beta_nx_n + \mathbf{\epsilon_{ij}}
\end{equation}
\end{document}
which this time yields:

You can even easily extend that code to fade the color from slide to slide and highlight one term at a time if you're using beamer (just add a \temporal<+> before the \stackrel, duplicate the \stackrel code three times and change the colors in each variant).