Add vertical line to a pgfplots histogram

A few examples:

documentclass{article}
usepackage{pgfplots}
begin{document}
If you really have 1,2,... as ticklabels, you can just remove the symbolic coordinates and use axis cs:
begin{center}
begin{tikzpicture}
  begin{axis}[ybar stacked, %symbolic x coords={1,2,3,4,5},
    xtick=data, ymin=0, bar width=30pt]
  addplot[ybar,fill=lightgray] coordinates {
    (1,3) (2,2) (3,1) (4,5) (5,3) };
draw (axis cs:3.5,0) -- (axis cs:3.5,5.5);,
end{axis}
end{tikzpicture}
end{center}

Or add compat=11 (or higher) and don't use axis cs:
begin{center}
pgfplotsset{compat=1.11} % normally add this to preamble
begin{tikzpicture}
  begin{axis}[ybar stacked, %symbolic x coords={1,2,3,4,5},
    xtick=data, ymin=0, bar width=30pt]
  addplot[ybar,fill=lightgray] coordinates {
    (1,3) (2,2) (3,1) (4,5) (5,3) };
draw (3.5,0) -- (3.5,5.5);,
end{axis}
end{tikzpicture}
end{center}

If you have non-numeric ticklabels, use xticklabels instead of symbolic coordinates:
begin{center}
begin{tikzpicture}
  begin{axis}[ybar stacked, xticklabels={foo,bar,baz,baa,abc},
    xtick=data, ymin=0, bar width=30pt]
  addplot[ybar,fill=lightgray] coordinates {
    (1,3) (2,2) (3,1) (4,5) (5,3) };
draw (axis cs:3.5,0) -- (axis cs:3.5,5.5);,
end{axis}
end{tikzpicture}
end{center}

Instead of manually specifying a y-coordinate you can access the value used in the axis with pgfkeysvalueof:
begin{center}
begin{tikzpicture}
  begin{axis}[ybar stacked, xticklabels={foo,bar,baz,baa,abc},
    xtick=data, ymin=0, bar width=30pt]
  addplot[ybar,fill=lightgray] coordinates {
    (1,3) (2,2) (3,1) (4,5) (5,3) };
draw (axis cs:3.5,pgfkeysvalueof{/pgfplots/ymin}) -- (axis cs:3.5,pgfkeysvalueof{/pgfplots/ymax});,
end{axis}
end{tikzpicture}
end{center}


end{document}