You can first define a "6 on 1" pgf page layout, then activate it in, say, the handout
mode. I use the code below -- I've probably modified it from somewhere but I can't remember. Perhaps you can fine tune it further for your own needs:
\documentclass[handout]{beamer}
\usetheme{Dresden}
\usepackage{pgfpages}
\pgfpagesdeclarelayout{6 on 1}
{
\edef\pgfpageoptionheight{\the\paperwidth} % landscaped by default
\edef\pgfpageoptionwidth{\the\paperheight}
\def\pgfpageoptionborder{0pt}
\def\pgfpageoptionfirstshipout{1}
}
{
\pgfpagesphysicalpageoptions
{%
logical pages=6,%
physical height=\pgfpageoptionheight,%
physical width=\pgfpageoptionwidth,%
current logical shipout=\pgfpageoptionfirstshipout%
}
\ifdim\paperheight>\paperwidth\relax
% put side-by-side
\pgfpageslogicalpageoptions{1}
{%
border shrink=\pgfpageoptionborder,%
resized width=.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.1667\pgfphysicalwidth}{.25\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{3}
{%
border shrink=\pgfpageoptionborder,%
resized width=.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.5\pgfphysicalwidth}{.25\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{5}
{%
border shrink=\pgfpageoptionborder,%
resized width=.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.8333\pgfphysicalwidth}{.25\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{2}
{%
border shrink=\pgfpageoptionborder,%
resized width=.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.1667\pgfphysicalwidth}{.75\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{4}
{%
border shrink=\pgfpageoptionborder,%
resized width=.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.5\pgfphysicalwidth}{.75\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{6}
{%
border shrink=\pgfpageoptionborder,%
resized width=.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.8333\pgfphysicalwidth}{.75\pgfphysicalheight}%
}%
\else
% stack on top of one another
\pgfpageslogicalpageoptions{1}
{%
border shrink=\pgfpageoptionborder,%
resized width=0.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.25\pgfphysicalwidth}{.8333\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{3}
{%
border shrink=\pgfpageoptionborder,%
resized width=0.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.25\pgfphysicalwidth}{.5\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{5}
{%
border shrink=\pgfpageoptionborder,%
resized width=0.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.25\pgfphysicalwidth}{.1667\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{2}
{%
border shrink=\pgfpageoptionborder,%
resized width=0.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.75\pgfphysicalwidth}{.8333\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{4}
{%
border shrink=\pgfpageoptionborder,%
resized width=0.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.75\pgfphysicalwidth}{.5\pgfphysicalheight}%
}%
\pgfpageslogicalpageoptions{6}
{%
border shrink=\pgfpageoptionborder,%
resized width=0.5\pgfphysicalwidth,%
resized height=\pgfphysicalheight,%
center=\pgfpoint{.75\pgfphysicalwidth}{.1667\pgfphysicalheight}%
}%
\fi
}
\mode<handout>{
\pgfpagesuselayout{6 on 1}[a4paper, border shrink=8mm]
\pgfpageslogicalpageoptions{1}{border code=\pgfusepath{stroke}}
\pgfpageslogicalpageoptions{2}{border code=\pgfusepath{stroke}}
\pgfpageslogicalpageoptions{3}{border code=\pgfusepath{stroke}}
\pgfpageslogicalpageoptions{4}{border code=\pgfusepath{stroke}}
\pgfpageslogicalpageoptions{5}{border code=\pgfusepath{stroke}}
\pgfpageslogicalpageoptions{6}{border code=\pgfusepath{stroke}}
}
\begin{document}
\begin{frame}{First}
lala
\end{frame}
\begin{frame}{Second}
lala
\end{frame}
\begin{frame}{Third}
lala
\end{frame}
\begin{frame}{Fourth}
lala
\end{frame}
\begin{frame}{Fifth}
lala
\end{frame}
\begin{frame}{Sixth}
lala
\end{frame}
\end{document}