Help aligning tables

A solution for both variants, two and three subfloats

\documentclass{article}
\usepackage{subfig}
\begin{document}

\begin{table}
\minipage[b]{0.49\linewidth}
 \centering
 \subfloat[]{%
 \begin{tabular}[b]{cc}\hline
        0 & 1\\\hline
        2 & 1\\
        3 & 1\\
        4 & 2\\
        5 & 3\\
        4 & 8\\\hline
 \end{tabular}}%
 \quad
 \subfloat[]{%
 \begin{tabular}[b]{@{}c@{}}%
    \begin{tabular}{ccc} \hline
       1 & 2 & 3\\ 
       3 & 7 & 4\\
       4 & 5 & 4\\\hline
    \end{tabular}\\[5ex]
    \begin{tabular}[b]{ccc} \hline
       1 & 2 & 3\\ 
       3 & 7 & 4\\
       4 & 5 & 4
    \end{tabular}\\\hline
  \end{tabular}}%
\caption{the one for all}

\endminipage\hfill
\minipage[b]{0.49\linewidth}
 \centering
 \subfloat[]{%
 \begin{tabular}[b]{cc}\hline
        0 & 1\\\hline
        2 & 1\\
        3 & 1\\
        4 & 2\\
        5 & 3\\
        4 & 8\\\hline
 \end{tabular}}%
 \quad
 \begin{tabular}[b]{c}%
 \subfloat[]{%
    \begin{tabular}{ccc} \hline
       1 & 2 & 3\\ 
       3 & 7 & 4\\
       4 & 5 & 4\\\hline
    \end{tabular}}\\[5ex]
 \subfloat[]{%
    \begin{tabular}[b]{ccc} \hline
       1 & 2 & 3\\ 
       3 & 7 & 4\\
       4 & 5 & 4\\\hline
    \end{tabular}}%
  \end{tabular}%

\caption{the one for all}
\endminipage
\end{table}

\end{document}

Use tabulars inside tabulars:

\documentclass{article}

\usepackage{subfig}

\begin{document}

\begin{table}
 \centering
  \subfloat[]{% 
    \begin{tabular}[b]{c}
    \begin{tabular}[b]{cc}
        \hline
        0 & 1\\
        \hline
        2 & 1\\
        3 & 1\\
        4 & 2\\
        5 & 3\\
        4 & 8\\
        \hline
    \end{tabular}%
    \end{tabular}%
  }
  \quad
  \subfloat[]{% 
    \begin{tabular}[b]{c}%
        \begin{tabular}{ccc} 
            \hline
            1 & 2 & 3\\ 
            3 & 7 & 4\\
            4 & 5 & 4\\
            \hline
            \end{tabular}
        \\\\%
        \begin{tabular}[b]{ccc} 
            \hline
            1 & 2 & 3\\ 
            3 & 7 & 4\\
            4 & 5 & 4\\
            \hline
        \end{tabular}%
        \\
    \end{tabular}%
  }%
\end{table}
\end{document}

Note, that the both parent and bottom tabular have a [b] argument. The left tabular must also be placed inside a parent tabular to get the same spacing to the subfloat label.

/edit: removed { } for inner tabulars.

Results:

Without left parent tabular:

With left parent tabular:

The added margins can be removed by replacing {c} with {@{}c@{}} in the parent tabulars.