I used the following code, but \circlearrowleft looks no good in this diagram. I would like to know if there is a better way to indicate the commutativity. Also, is there any way to indicate non-commutativity?
\begin{equation*}
\xymatrix@-1.75pc{
\overline{A} \ar[dd]_{\overline{F}_q} & & \overline{A}_E
\ar[dd]^{\overline{F}_{q,E}} \ar[ll]_{\pi^{\ast}} \\
& \circlearrowleft & \\
\overline{A} & & \overline{A}_E \ar[ll]^{\pi^{\ast}}
}
\end{equation}

\circlearrowleftin the diagram? It may be a bit ugly but it is the usual way to emphasise commutativity. As for non-commutativity then I agree with salvor7 below that the default assumption is that the diagram commutes and I don't know of a standard way of indicating otherwise. One option would be to ask on Maths-SX if there is a standard and then if one emerges to ask how to typeset it here. When I've had to do a non-commuting diagram I've used linguistics as salvor7 says: "We have the following (non-commuting!) diagram". – Andrew Stacey Feb 21 '13 at 09:39