Just use the following style file and your appendix is counted separately, and the "real" total slide count is adapted automatically as well.  appendixnumberbeamer.sty

In case the link doesn't work anymore:

%% J�r�me Lelong (September 2007)
%% 
%% this stuff fixes the frame numbering in beamer when using an appendix such
%% that the slides of the appendix are not counted in the total framenumber


\makeatletter


\let\appendixtotalframenumber\empty
\def\mainend{-1}
\let\appendixorig\appendix

\def\appendix{
  \edef\mainend{\theframenumber}
  \immediate\write\@auxout{\string\global\string\@namedef{mainendframenumber}{\mainend}}
  \appendixorig
  \def\inserttotalframenumber{\appendixtotalframenumber}%
  \setcounter{framenumber}{0}
}

\def\pageatend{
  \edef\appendixend{\theframenumber}
  \ifnum\mainend>0%
  \immediate\write\@auxout{\string\global\string\@namedef{appendixtotalframenumber}{\appendixend}}%
  \immediate\write\@auxout{\string\global\string\@namedef{inserttotalframenumber}{\mainend}}%
  \immediate\write\@auxout{\string\@writefile{nav}{\noexpand \headcommand {%
        \noexpand \def\noexpand \inserttotalframenumber{\mainend}}}}%
  \immediate\write\@auxout{\string\@writefile{nav}{\noexpand \headcommand {%
        \noexpand \def\noexpand \appendixtotalframenumber{\appendixend}}}}%
  \else
  \fi
}


\AtEndDocument{\pageatend}
\makeatother