The following works for me:
\begin{table}[htdp] \begin{center} \begin{tabular}{|c|c|c|} \hline & PatAddTTCoord & AddTTClusterTool\\ \hline hit-efficiency\footnotemark & 93.2 \% & 90.6 \% \\ \hline \end{tabular} \end{center} \label{tb:comp1} \end{table}% \footnotetext[\value{footnote}]{Hit-efficiency is defined in section \ref{sec:effdef}}