Qcircuit

If Qcircuit was previously working and suddenly stopped, the most likely cause is that you are using Xy-pic version 3.8 or later with Qcircuit version 1.2 or earlier. You should switch to version 2 or later of the package. Use the qcircuit.sty file (not the old Qcircuit.tex).

No. A label is treated as a kind of gate command, so you can't put a label and a gate in the same entry — just like you can't put two gates in the same entry. Each circuit entry holds exactly one element.

Labels are treated as having zero size, which prevents them from affecting the circuit layout but also means they are not considered when calculating the circuit's bounding box. Use this hack for labels that stick out:

\Qcircuit @C=1em @R=1em {
  \push{\rule{0em}{1em}} & & \dstick{label} \\
  \push{\rule{2em}{0em}} & \lstick{label} & \gate{A}
}

For rough positioning, use \dstick or \ustick. For precise vertical placement, use \raisebox:

\Qcircuit @C=1em @R=1em {
  & \gate{A} & \qw & & &\gate{B} & \qw \\
  & \gate{C} & \qw & \raisebox{2em}{=} & &\gate{D} & \qw
}

Place the \Qcircuit command inside a \mbox{}, an equation environment, or a \centerline{}. If all else fails, try \centering followed by \leavevmode inside the figure environment.

\begin{figure}[h]
  \mbox{
    \Qcircuit @C=1em @R=1em { & \gate{X} & \qw }
  }
  \caption{NOT Gate}
\end{figure}

Using $...$ centers the top row. For full vertical centering, use the array environment:

$\begin{array}{c}
  \Qcircuit @C=1em @R=1em {
    & \gate{X} & \qw
  }
\end{array}$

LaTeX views the wires and gate outlines as a single object, so you cannot color them separately. You can color the entire circuit or any text argument in the normal manner using the xcolor package.