I would agree that row colour is a great addition to tables, since it is much more subtle than horizontal rules. And by subtle I refer to the use of a colour that is not too bold - using a shade of black or grey is best since it has dual purpose in colour (on-screen) and black-and-white environments (printing).
When alternately colouring rows of a table and using a heading colour (perhaps darker), start colouring the second row of the table body rather than the first:

Perhaps, playing devil's advocate, here is an example of where row colours may cause problems. The concern is consistency and aesthetics:

For example, do you colour rows only from column 2-4? Or do you colour each "Approach" group (in this case it trivially defaults to only colouring rows 3-4 in the table body)? Or do you colour the first column with the same row colour and keep the row colours as-is?
\documentclass{article}
\usepackage{booktabs}% http://ctan.org/pkg/booktabs
\usepackage{colortbl}% http://ctan.org/pkg/colortbl
\usepackage{amsmath}% http://ctan.org/pkg/amsmath
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
\usepackage{graphicx}% http://ctan.org/pkg/graphicx
\colorlet{tableheadcolor}{gray!25} % Table header colour = 25% gray
\newcommand{\headcol}{\rowcolor{tableheadcolor}} %
\colorlet{tablerowcolor}{gray!10} % Table row separator colour = 10% gray
\newcommand{\rowcol}{\rowcolor{tablerowcolor}} %
% Command \topline consists of a (slightly modified) \toprule followed by a \heavyrule rule of colour tableheadcolor (hence, 2 separate rules)
\newcommand{\topline}{\arrayrulecolor{black}\specialrule{0.1em}{\abovetopsep}{0pt}%
\arrayrulecolor{tableheadcolor}\specialrule{\belowrulesep}{0pt}{0pt}%
\arrayrulecolor{black}}
% Command \midline consists of 3 rules (top colour tableheadcolor, middle colour black, bottom colour white)
\newcommand{\midline}{\arrayrulecolor{tableheadcolor}\specialrule{\aboverulesep}{0pt}{0pt}%
\arrayrulecolor{black}\specialrule{\lightrulewidth}{0pt}{0pt}%
\arrayrulecolor{white}\specialrule{\belowrulesep}{0pt}{0pt}%
\arrayrulecolor{black}}
% Command \rowmidlinecw consists of 3 rules (top colour tablerowcolor, middle colour black, bottom colour white)
\newcommand{\rowmidlinecw}{\arrayrulecolor{tablerowcolor}\specialrule{\aboverulesep}{0pt}{0pt}%
\arrayrulecolor{black}\specialrule{\lightrulewidth}{0pt}{0pt}%
\arrayrulecolor{white}\specialrule{\belowrulesep}{0pt}{0pt}%
\arrayrulecolor{black}}
% Command \rowmidlinewc consists of 3 rules (top colour white, middle colour black, bottom colour tablerowcolor)
\newcommand{\rowmidlinewc}{\arrayrulecolor{white}\specialrule{\aboverulesep}{0pt}{0pt}%
\arrayrulecolor{black}\specialrule{\lightrulewidth}{0pt}{0pt}%
\arrayrulecolor{tablerowcolor}\specialrule{\belowrulesep}{0pt}{0pt}%
\arrayrulecolor{black}}
% Command \rowmidlinew consists of 1 white rule
\newcommand{\rowmidlinew}{\arrayrulecolor{white}\specialrule{\aboverulesep}{0pt}{0pt}%
\arrayrulecolor{black}}
% Command \rowmidlinec consists of 1 tablerowcolor rule
\newcommand{\rowmidlinec}{\arrayrulecolor{tablerowcolor}\specialrule{\aboverulesep}{0pt}{0pt}%
\arrayrulecolor{black}}
% Command \bottomline consists of 2 rules (top colour
\newcommand{\bottomline}{\arrayrulecolor{white}\specialrule{\aboverulesep}{0pt}{0pt}%
\arrayrulecolor{black}\specialrule{\heavyrulewidth}{0pt}{\belowbottomsep}}%
\newcommand{\bottomlinec}{\arrayrulecolor{tablerowcolor}\specialrule{\aboverulesep}{0pt}{0pt}%
\arrayrulecolor{black}\specialrule{\heavyrulewidth}{0pt}{\belowbottomsep}}%
\begin{document}
\renewcommand{\arraystretch}{1.5}
\begin{tabular}{llll}
\topline
\headcol Approach & Estimator & ME & MAE \\
\midline
& $\widehat{JV}_{\text{na\"ive}}$ & 4.37e-07 & 4.37e-07 \\
\rowcol \smash{\raisebox{1em}{Na\"ive}} & $\widetilde{JV}_{\text{na\"ive}}$ & 3.88e-07 & 3.88e-07 \\
& $\widehat{JV}$ & 1.33e-06 & 1.33e-06 \\
\rowcol \smash{\raisebox{1em}{Regular}} & $\widetilde{JV}$ & 1.20e-06 & 1.20e-06 \\
\bottomlinec
\end{tabular}
\end{document}
The above code includes a number of additional line definitions based on \specialrule
from booktabs
. It allows for specifying a colour for the table header (tableheadcolor
) and table body row (tablerowcolor
), depending on whether your row is coloured or not and/or ending/beginning with a coloured row or not.
As similar, perhaps less manual approach, is obtainable using tabu
or tikz/pgf
for that matter.
booktabs
and alternating row colors looks good.