In the following example I define a new command \CFTable with one optional argument, which redefines the table and table* environments as defined by the standard document classes; the optional argument will select the font size switch to be applied to the tables (it will not have any effect on the captions); the valid values for the optional argument are tiny, scriptsize, footnotesize, small (default), normalsize, large, Large, LARGE, huge, and Huge:
\RequirePackage{filecontents}
\begin{filecontents*}{testtables.tex}
\begin{table}
\centering
\caption{Some test table}
\begin{tabular}{cc}
text & text \\
123 & 234\\
123 & 234\\
123 & 234\\
123 & 234\\
123 & 234\\
\end{tabular}
\end{table}
\end{filecontents*}
\documentclass{article}
\makeatletter
\newcommand\CTFont[1][small]{
\renewenvironment{table}
{\@float{table}\csname#1\endcsname}
{\end@float}
\renewenvironment{table*}
{\@dblfloat{table}\csname#1\endcsname}
{\end@dblfloat}
}
\makeatother
\begin{document}
\begingroup
\CTFont% tables in \small size
\input{testtables}
\endgroup
\begingroup
\CTFont[tiny]% tables in \tiny size
\input{testtables}
\endgroup
\begingroup
\CTFont[Large]% tables in \Large size
\input{testtables}
\endgroup
\end{document}

The filecontents package and the filecontents* environment are only to provide a complete compilable example; you don't need them in your actual code.
With the code above, the change in the font size will only affect the table contents but not the captions; to achieve a simultaneous change to the caption font size, it's enough to load the caption package:
\usepackage{caption}
and change the definition of \CFTable to
\makeatletter
\newcommand\CTFont[1][small]{
\captionsetup[table]{font=#1}
\renewenvironment{table}
{\@float{table}\csname#1\endcsname}
{\end@float}
\renewenvironment{table*}
{\@dblfloat{table}\csname#1\endcsname}
{\end@dblfloat}
}
\makeatother
now, however, the only valid values for the optional argument are scriptsize, footnotesize, small (default), normalsize, large, and Large.
tabularonly, or also that of the caption? – Werner Nov 11 '11 at 4:22tabularonly, but either is okay. – FEQ Nov 11 '11 at 4:23\inputfile or not. Your issue here is that thetableenvironment changes the font itself. – Martin Scharrer♦ Nov 11 '11 at 16:31