You can use the overlay and remember picture attributes of tikz/pgf to mark elements within your listings, and draw the lines after typesetting them. To do this, you can momentarily "escape" the listing formatting via mathescape=true to mark a specific location. Here's a minimal example:

\documentclass[a4paper,10pt]{report}
\usepackage{fullpage}% http://ctan.org/pkg/fullpage
\usepackage{listings}% http://ctan.org/pkg/listings
\usepackage{parcolumns}% http://ctan.org/pkg/parcolumns
\usepackage{textcomp}% http://ctan.org/pkg/textcomp
\usepackage{tikz}% http://ctan.org/pkg/pgf
\usetikzlibrary{calc}
% http://tex.stackexchange.com/questions/1559/adding-a-large-brace-next-to-a-body-of-text/1570#1570
\newcommand{\tikzmark}[1]{\tikz[overlay,remember picture] \node (#1) {};}
\lstset{
language=C,
keywordstyle=\bfseries\ttfamily\color[rgb]{0,0,1},
identifierstyle=\ttfamily,
commentstyle=\color[rgb]{0.133,0.545,0.133},
stringstyle=\ttfamily\color[rgb]{0.627,0.126,0.941},
showstringspaces=false,
basicstyle=\small,
numberstyle=\footnotesize,
stepnumber=1,
numbersep=10pt,
tabsize=2,
breaklines=true,
prebreak = \raisebox{0ex}[0ex][0ex]{\ensuremath{\hookleftarrow}},
breakatwhitespace=false,
aboveskip={1.5\baselineskip},
columns=fixed,
upquote=true,
extendedchars=true,
frame=single,
mathescape % Allows escaping to (La)TeX mode within $..$
}
\begin{document}
\begin{parcolumns}[nofirstindent]{2}
\colchunk{
\noindent\begin{minipage}{.45\textwidth}
\begin{lstlisting}[language={[x86masm]Assembler},caption={Original code},label={lst:OrigCode}]
1 $\tikzmark{L1line1}$
2
3
4 $\tikzmark{L1line4}$
5
..
12
\end{lstlisting}
\end{minipage}
}
\colchunk{
\begin{minipage}{.45\textwidth}
\begin{lstlisting}[language={[x86masm]Assembler},caption={Code after insertion of detour},label={lst:AfterDetour}]
$\tikzmark{L2line1}$ 86
$\tikzmark{L2line4}$ 4
5
..
12
\end{lstlisting}
\end{minipage}
}
\colplacechunks
\end{parcolumns}
\tikz[overlay,remember picture] \draw[color=red] ($(L1line1)+(0pt,0.7ex)$) -- ($(L2line1)+(0pt,0.7ex)$);
\tikz[overlay,remember picture] \draw[color=blue] ($(L1line4)+(0pt,0.7ex)$) -- ($(L2line4)+(0pt,0.7ex)$);
\end{document}
While in "math escape mode", you can execute any (La)TeX commands. We just use this opportunity to set the \tikzmark that we use later.
The placement and alignment of the nodes are up to you. A similar approach is possible using pst-node from the pstricks bundle, but would require a latex->dvips->ps2pdf or xelatex compiling sequence. Here is a duplication of the above approach using pstricks, which produces the identical output:
\documentclass[a4paper,10pt]{report}
\usepackage{fullpage}% http://ctan.org/pkg/fullpage
\usepackage{listings}% http://ctan.org/pkg/listings
\usepackage{parcolumns}% http://ctan.org/pkg/parcolumns
\usepackage{textcomp}% http://ctan.org/pkg/textcomp
\usepackage{pst-node}% http://ctan.org/pkg/pst-node
\lstset{
language=C,
keywordstyle=\bfseries\ttfamily\color[rgb]{0,0,1},
identifierstyle=\ttfamily,
commentstyle=\color[rgb]{0.133,0.545,0.133},
stringstyle=\ttfamily\color[rgb]{0.627,0.126,0.941},
showstringspaces=false,
basicstyle=\small,
numberstyle=\footnotesize,
stepnumber=1,
numbersep=10pt,
tabsize=2,
breaklines=true,
prebreak = \raisebox{0ex}[0ex][0ex]{\ensuremath{\hookleftarrow}},
breakatwhitespace=false,
aboveskip={1.5\baselineskip},
columns=fixed,
upquote=true,
extendedchars=true,
frame=single,
mathescape % Allows escaping to (La)TeX mode within $..$
}
\begin{document}
\begin{parcolumns}[nofirstindent]{2}
\colchunk{
\noindent\begin{minipage}{.45\textwidth}
\begin{lstlisting}[language={[x86masm]Assembler},caption={Original code},label={lst:OrigCode}]
1 $\rnode[r]{L1line1}{\strut}$
2
3
4 $\rnode[r]{L1line4}{\strut}$
5
..
12
\end{lstlisting}
\end{minipage}
}
\colchunk{
\begin{minipage}{.45\textwidth}
\begin{lstlisting}[language={[x86masm]Assembler},caption={Code after insertion of detour},label={lst:AfterDetour}]
$\rnode[l]{L2line1}{\strut}$ 86
$\rnode[l]{L2line4}{\strut}$ 4
5
..
12
\end{lstlisting}
\end{minipage}
}
\colplacechunks
\end{parcolumns}
\psline[linecolor=red](L1line1)(L2line1)
\psline[linecolor=blue](L1line4)(L2line4)
\end{document}