Two logos in opposite side on beamer

Try

\logo{%
  \makebox[0.95\paperwidth]{%
    \includegraphics[width=1cm,keepaspectratio]{cern_logo_white.jpg}%
    \hfill%
    \includegraphics[width=1cm,keepaspectratio]{ntua-logo.jpg}%
  }%
}

It seems that logos are put at 2.5pt from the right slide edge as Paul Gaborit found out. Thus \paperwidth-5pt might be the correct size to be given to the LaTeX box.

Since the textpos package has already been loaded, the task is not so difficult. Similarly to the answer in Positioning logo in the front page as well as slides the second logo has been positioned by adding it to a pre-existent template, headline in this case.

Code:

\documentclass[compress,mathserif,12pt,xcolor=dvipsnames]{beamer}
\definecolor{LHCblue}{RGB}{4, 114, 255}
\usecolortheme[named=LHCblue]{structure}
\usepackage[bars]{beamerthemetree} % Beamer theme v 2.2
\usepackage{kerkis}
\usepackage{multimedia}
\usepackage{subfigure}
\mode<presentation>
\newcommand*\oldmacro{}%
\let\oldmacro\insertshorttitle%
\renewcommand*\insertshorttitle{%
  \oldmacro\hfill%
  \insertframenumber\,}%/\,\inserttotalframenumber
\setbeamertemplate{footline}[frame number]
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\setbeamercovered{higly dynamic}
\usetheme{Ilmenau} % Beamer theme v 3.0
\useoutertheme[subsection=true]{smoothbars}%Beamer Outer Theme-circles on top
\useinnertheme{circles} %rectangle bullet points instead of circle ones
\usepackage{beamerthemebars}
\setbeamercolor{navigation symbols dimmed}{fg=red!80!black}
\setbeamercolor{navigation symbols}{fg=red!80!black}
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\title{July 2012 H4 Test Beam}
\author[Stamatopoulos N. Athanasios\hspace{2.5cm}{[email protected]}]    {Stamatopoulos N. Athanasios}
\institute{NTUA/CERN}

\logo{%
    \includegraphics[width=1cm,height=1cm,keepaspectratio]{ntua-logo}%
}
\usepackage{textpos}
\addtobeamertemplate{headline}{}{%
\begin{textblock*}{100mm}(.015\textwidth,0.2cm)
\includegraphics[height=1cm,width=1cm]{logopolito} % logo of my university
\end{textblock*}}

\begin{document}

\begin{frame}
\titlepage
\end{frame}

\begin{frame}
Good Morning Vietnam!!!
\end{frame}

\end{document} 

Result:

Here is a solution using \hspace to add space between logos.

Given that the paper width is \paperwidth, each logo has a width of 1cm, the margin between the edge and a logo is 2.5pt, the length of the space must be \paperwidth-2cm-5pt.

\documentclass[slidestop,compress,mathserif,12pt,xcolor=dvipsnames]{beamer}
\definecolor{LHCblue}{RGB}{4, 114, 255}
\usecolortheme[named=LHCblue]{structure}
\usepackage[bars]{beamerthemetree} % Beamer theme v 2.2
\usepackage{kerkis}
\usepackage{multimedia}
\usepackage{subfigure}
%\usepackage{calc}
\mode<presentation>
\newcommand*\oldmacro{}%
\let\oldmacro\insertshorttitle%
\renewcommand*\insertshorttitle{%
  \oldmacro\hfill%
  \insertframenumber\,}%/\,\inserttotalframenumber
\setbeamertemplate{footline}[frame number]
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\setbeamercovered{higly dynamic}
\usetheme{Ilmenau} % Beamer theme v 3.0
\useoutertheme[subsection=true]{smoothbars}%Beamer Outer Theme-circles on top
\useinnertheme{circles} %rectangle bullet points instead of circle ones
\usepackage{beamerthemebars}
\setbeamercolor{navigation symbols dimmed}{fg=red!80!black}
\setbeamercolor{navigation symbols}{fg=red!80!black}
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\title{July 2012 H4 Test Beam}
\author[Stamatopoulos N. Athanasios\hspace{2.5cm}{[email protected]}]    {Stamatopoulos N. Athanasios}
\institute{NTUA/CERN}
\logo{%
  \includegraphics[width=1cm,height=1cm,keepaspectratio]{example-image}%
  \hspace{\dimexpr\paperwidth-2cm-5pt}%
  \includegraphics[width=1cm,height=1cm,keepaspectratio]{example-image}%
}
\usepackage{textpos}

\begin{document}

\begin{frame}
\titlepage
\end{frame}

\begin{frame}
Good Morning Vietnam!!!
\end{frame}

\end{document}