The standard at my university was to draw the diagram in LaTex.
You can pretty easily make a flow diagram with TikZ and PGF:
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{shapes,arrows}
\begin{document}
\pagestyle{empty}
% Define styles
\tikzstyle{block} = [rectangle, draw, fill=blue!20,
text width=5em, text centered, rounded corners, minimum height=4em]
\tikzstyle{line} = [draw, -latex']
\tikzstyle{cloud} = [draw, ellipse,fill=red!20, node distance=3cm,
minimum height=2em]
\begin{tikzpicture}[node distance = 2cm, auto]
% Place nodes
\node [block] (model) {Model};
\node [block, below left of=model, node distance=4cm] (view) {View};
\node [block, below right of=model, node distance=4cm] (controller) {Controller};
\node [cloud, below right of=view] (user) {User};
% Draw edges
\path [line] (model) -| node [near start] {Updates} (view);
\path [line] (controller) |- node [near start] {Manipulates} (model);
\path [line] (view) -- node {Sees} (user);
\path [line] (user) -- node {Uses} (controller);
\end{tikzpicture}
\end{document}
results in:
.