The pgfplotstable package allows you to use the facilities of the array package (provided it is loaded) and allows you to either use custom column types (as explained in the array documentation), or to add the the existing specification of a column.
The array package allows you to specify code at the beginning and end of each cell in a column. See this question for details on how that works.
pgfplotstable provides hooks into this using the column type key. Here's example. I've shown how to make each column have a different size, and also how to make the column header have a different size from the rest of the column.
\documentclass{article}
\usepackage{pgfplotstable}
\usepackage{array}
\begin{filecontents}{\jobname.csv}
A, B
1,100
2,200
3,300
4,400
\end{filecontents}
\begin{document}
\pgfplotstabletypeset
[col sep=comma,
columns/A/.style=
{column type/.add={>{\Large}}{}},
columns/B/.style=
{column type/.add={>{\small}}{},
column name={\Huge B}}
]{\jobname.csv}
\end{document}

pgfplotstable-- getting an idea from you as to how you'd like to organize the table's structure would be very helpful. – Mico Aug 17 '13 at 13:33user...:-) – Joseph Wright Aug 17 '13 at 13:47