How to move text labels vertically in tikztiming

Here, I place the text in equal sized \makeboxes. The \small can be inside or outside of the \makebox, though a slightly different gap will result after the text, depending...

Why the original version of the OP behaves thus, it might be a case of right-aligned labels.

\documentclass[border=2mm]{standalone}
\usepackage{tikz}
\usepackage{tikz-timing}
\begin{document}
\begin{tikztimingtable}[%
    timing/dslope=0.1,
    timing/.style={x=5ex,y=2.2ex},
    x=1ex,
    timing/rowdist=3ex,
    timing/name/.style={font=\rmfamily}]
\makebox[5ex]{\small Data}   & {[semitransparent]3u} 2D{0} 2D{1}  2D{1} 2D{0} {[semitransparent]2u}\\
\makebox[5ex]{\small Clock}  & {[semitransparent]3u} LHLHLHLH {[semitransparent]2u}\\ \\
\end{tikztimingtable}
\end{document}

The above MWE fixes the horizontal centering of the two words. To also fix the vertical alignment, per follow-up comments, one can combine this result with a \raisebox:

\documentclass[border=2mm]{standalone}
\usepackage{tikz}
\usepackage{tikz-timing}
\begin{document}
\begin{tikztimingtable}[%
    timing/dslope=0.1,
    timing/.style={x=5ex,y=2.2ex},
    x=1ex,
    timing/rowdist=3ex,
    timing/name/.style={font=\rmfamily}]
\raisebox{1.5pt}{\makebox[5ex]{\small Data}}   & {[semitransparent]3u} 2D{0} 2D{1}  2D{1} 2D{0} {[semitransparent]2u}\\
\raisebox{1.5pt}{\makebox[5ex]{\small Clock}}  & {[semitransparent]3u} LHLHLHLH {[semitransparent]2u}\\ \\
\end{tikztimingtable}
\end{document}

A little yshift added to the timing/name style. Also, I'd move the \small there as well.

\documentclass[border=2mm]{standalone}
\usepackage{tikz}
\usepackage{tikz-timing}
\begin{document}
\begin{tikztimingtable}[%
    timing/dslope=0.1,
    timing/.style={x=5ex,y=2.2ex},
    x=1ex,
    timing/rowdist=3ex,
    timing/name/.style={font=\rmfamily\small,yshift=2pt}]
Data   & {[semitransparent]3u} 2D{0} 2D{1}  2D{1} 2D{0} {[semitransparent]2u}\\
Clock  & {[semitransparent]3u} LHLHLHLH {[semitransparent]2u}\\ \\
\end{tikztimingtable}
\end{document}