\documentclass{article}
\usepackage{amsmath}
\usepackage{xypic}

% thats a demo for putting a symbol in the center of a square diagram!

\newcommand{\refsymbol}{{?}}

\begin{document}
Here we have a diagram.
		\begin{equation}
			\xymatrix{
			  A \ar[r] \ar[d]
			  \ar@{}[dr] | {\refsymbol}
			  & B \ar[d] \\
			  C \ar[r] & D
			}
		\label{eq:diag}
	\end{equation}
We want to refer to {\refsymbol} in the square shown in \eqref{eq:diag}.
\end{document}