Creating a very flexible TOC with beamer

You can use the multicol package to switch to two-column mode for the ToCs; the color for certain parts can be changed by setting the appropriate template or color template. A little example with two-column ToCs and with a variation of the color for the sections in the upper navigation bar, and the sections in the partial ToCs at the beginning of each section:

\documentclass[compress]{beamer}
\usetheme{Warsaw}
\usepackage{multicol}

\colorlet{mycolor}{orange!80!black}% change this color to suit your needs

\title[Intro. to High-Perf. Computing ]{Introduction to\\ High-Performance Computing with R\\
\small Tutorial at \textit{useR! 201}}
\author{The Author}
\AtBeginSection[]{
  \setbeamercolor{section in toc shaded}{use=structure,fg=structure.fg}
  \setbeamercolor{section in toc}{fg=mycolor}
  \setbeamercolor{subsection in toc shaded}{fg=black}
  \setbeamercolor{subsection in toc}{fg=mycolor}
  \frame<beamer>{\begin{multicols}{2}
  \frametitle{Outline}
  \setcounter{tocdepth}{2}  
  \tableofcontents[currentsection,subsections]
\end{multicols} 
 }
}

\setbeamercolor{author in head/foot}{fg=white}
\setbeamercolor{title in head/foot}{fg=mycolor}
\setbeamercolor{section in head/foot}{fg=mycolor}
\setbeamertemplate{section in head/foot shaded}{\color{white!70!black}\insertsectionhead}
\setbeamercolor{subsection in head/foot}{fg=mycolor}
\setbeamertemplate{subsection in head/foot shaded}{\color{white!70!black}\insertsubsectionhead}
\setbeamercolor{frametitle}{fg=white}
\setbeamercolor{framesubtitle}{fg=white}

\begin{document}

\begin{frame}
\maketitle
\end{frame}

\section[]{Motivation}
\begin{frame}\frametitle{Some title1}Test\end{frame}
\begin{frame}\frametitle{Some title2}Test\end{frame}

\section[Tools]{Automation and Scripting}
\subsection{Overview}
\begin{frame}Test\end{frame}
\subsection{Littler}
\begin{frame}Test\end{frame}
\subsection{Rscript}
\begin{frame}Test\end{frame}

\section[Measure]{Measuring and Profiling}
\subsection{Overview}
\begin{frame}Test\end{frame}
\subsection{RProf}
\begin{frame}Test\end{frame}
\subsection{RProfmem}
\begin{frame}Test\end{frame}
\subsection[Profiling]{Profiling Compiled Code}
\begin{frame}Test\end{frame}
\subsection{Sumary}
\begin{frame}Test\end{frame}

\section[Faster]{Speeding up}
\subsection[Vec]{Vectorisation}
\begin{frame}Test\end{frame}
\subsection[Ra]{Just-in-time compilation}
\begin{frame}Test\end{frame}
\subsection{BLAS}
\begin{frame}Test\end{frame}
\subsection{GPUs}
\begin{frame}Test\end{frame}
\subsection{Summary}
\begin{frame}Test\end{frame}

\end{document}

This is the closer I could get, building on Gonzalo's answer. Notice the hideothersubsections as well as the beamertemplate. I couldn't make it so that subsections doesn't go over the other column.

\documentclass    [10pt, compress]{beamer}
\usetheme{Warsaw}
\usepackage{multicol}

\colorlet{mycolor}{orange!80!black}% change this color to suit your needs

\title[Intro. to High-Perf. Computing ]{Introduction to\\ High-Performance Computing with R\\
\small Tutorial at \textit{useR! 201}}
\author{The Author}
\AtBeginSection[]{
  \setbeamercolor{section in toc shaded}{use=structure,fg=structure.fg}
  \setbeamercolor{section in toc}{fg=mycolor}
  \setbeamercolor{subsection in toc shaded}{fg=black}
  \setbeamercolor{subsection in toc}{fg=mycolor}
  \setbeamertemplate{subsections in toc}[circle]
  \frame<beamer>{\begin{multicols}{2}
  \frametitle{Outline}
  \setcounter{tocdepth}{2}  
  \tableofcontents[currentsection,subsections,hideothersubsections]
\end{multicols} 
 }
}

\setbeamercolor{author in head/foot}{fg=white}
\setbeamercolor{title in head/foot}{fg=mycolor}
\setbeamercolor{section in head/foot}{fg=mycolor}
\setbeamertemplate{section in head/foot shaded}{\color{white!70!black}\insertsectionhead}
\setbeamercolor{subsection in head/foot}{fg=mycolor}
\setbeamertemplate{subsection in head/foot shaded}{\color{white!70!black}\insertsubsectionhead}
\setbeamercolor{frametitle}{fg=white}
\setbeamercolor{framesubtitle}{fg=white}

\begin{document}

\begin{frame}
\maketitle
\end{frame}

\section[]{Motivation}
\begin{frame}\frametitle{Some title1}Test\end{frame}
\begin{frame}\frametitle{Some title2}Test\end{frame}

\section[Tools]{Automation and Scripting}
\subsection{Overview}
\begin{frame}Test\end{frame}
\subsection{Littler}
\begin{frame}Test\end{frame}
\subsection{Rscript}
\begin{frame}Test\end{frame}

\section[Measure]{Measuring and Profiling}
\subsection{Overview}
\begin{frame}Test\end{frame}
\subsection{RProf}
\begin{frame}Test\end{frame}
\subsection{RProfmem}
\begin{frame}Test\end{frame}
\subsection[Profiling]{Profiling Compiled Code}
\begin{frame}Test\end{frame}
\subsection{Sumary}
\begin{frame}Test\end{frame}

\section[Faster]{Speeding up}
\subsection[Vec]{Vectorisation}
\begin{frame}Test\end{frame}
\subsection[Ra]{Just-in-time compilation}
\begin{frame}Test\end{frame}
\subsection{BLAS}
\begin{frame}Test\end{frame}
\subsection{GPUs}
\begin{frame}Test\end{frame}
\subsection{Summary}
\begin{frame}Test\end{frame}

\end{document}