Besides using booktabs, you can use either colortbl or xcolor (with the option [table] to color the tables.
\documentclass{article}
\usepackage[table]{xcolor}
\usepackage{booktabs}
\begin{document}
\begin{tabular}{*5l} \toprule
\emph{name} & \emph{foo} &&& \\\midrule
Models & A & B & C & D \\
\rowcolor{blue!50} Model $X$ & X1 & X2 & X3 & X4\\
\rowcolor{green!50} Model $Y$ & Y1 & Y2 & Y3 & Y4\\\bottomrule
\hline
\end{tabular}
\end{document}

Another method is somewhat automatic:
\rowcolors{<starting row>}{<first color>}{<second color>}
MWE:
\documentclass{article}
\usepackage[table]{xcolor}
\usepackage{booktabs}
\begin{document}
\rowcolors{3}{green!25}{yellow!50}
\begin{tabular}{ *5l } \toprule
\emph{name} & \emph{foo} &&& \\\midrule
Models & A & B & C & D \\
Model $X$ & X1 & X2 & X3 & X4\\
Model $Y$ & Y1 & Y2 & Y3 & Y4\\\bottomrule
\hline
\end{tabular}
\end{document}

Refer to the documentation of xcolor at texdoc.net for more details.
\\[3ptinstead of\\on the first line, and get rid of\hlineand|. – Benjamin McKay Jan 22 '13 at 10:21