Here's a little example: two "outer" nodes, each one containing a graph (formed with "inner" nodes) and some edges and arrows connecting outer nodes to outer nodes, and inner nodes from one graph to inner nodes of the other; the remember picture option lets you access inner and outer nodes at any time:
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{positioning,calc}
\begin{document}
\begin{tikzpicture}[remember picture,
inner/.style={circle,draw=blue!50,fill=blue!20,thick,inner sep=3pt},
outer/.style={draw=green,fill=green!20,thick,inner sep=10pt}
]
\node[outer,draw=green] (A) {
\begin{tikzpicture}
\node [inner,draw=blue] (ai) {A1};
\node [inner,draw=blue,below=of ai] (aii) {A2};
\node [inner,draw=blue,right=of aii] (aiii) {A3};
\draw[red,thick] (ai) -- (aii) -- (aiii) -- (ai);
\end{tikzpicture}
};
\node[outer,draw=green,right=of A] (B) {
\begin{tikzpicture}
\node [inner,draw=blue] (bi) {B1};
\node [inner,draw=blue,below=of bi] (bii) {B2};
\node [inner,draw=blue,right=of bii] (biii) {B3};
\node [inner,draw=blue,right=of bi] (biv) {B4};
\draw[red,thick] (bi) -- (bii) -- (biii) -- (biv) -- (bi) -- (biii);
\end{tikzpicture}
};
\draw[thick,orange,->] (ai) -- (bii);
\draw[orange,->] (aiii) -- (bi);
\draw[orange,->] (A.90) -- ($(A.90)+(0,1)$) -| (B);
\end{tikzpicture}
\end{document}

remember picturewas the key! Thanks! – gablin Sep 07 '11 at 19:11