When I run your example I get exactly what I expect and it's unclear to me what you want differently... as an aside I have a few comments on your code:
Code: Select all
\documentclass[12pt,a4paper]{report}
\usepackage[prefix]{nomencl}
\newcommand{\nomunit}[1]{\renewcommand{\nomentryend}{\hspace*{\fill}#1}}
\makenomenclature
\usepackage{makeidx}% <= not needed here
\makeindex% <= not needed here
\begin{document}
This is a minimal working example.\\ % <= don't use \\ if you want to end a
% paragraph! Leave an empty line instead
\printnomenclature
And this is the equation that changed the world's history:
\begin{center}% <= not needed here. equations are already centered
\begin{equation} \label{relat}
E=mc^2
\end{equation}
\end{center}
\nomenclature{$E$}{Energy\nomunit{J}}
\nomenclature{$m$}{Mass\nomunit{kg}}
\nomenclature{$c$}{Speed of light\nomunit{m/s}}
\end{document}
If I change the example according to my comments and run the file:
Code: Select all
% arara: pdflatex
% arara: nomencl
% arara: pdflatex
\documentclass[12pt,a4paper]{report}
\usepackage[prefix]{nomencl}
\newcommand{\nomunit}[1]{\renewcommand{\nomentryend}{\hspace*{\fill}#1}}
\makenomenclature
\begin{document}
This is a minimal working example.
\printnomenclature
And this is the equation that changed the world's history:
\begin{equation} \label{relat}
E=mc^2
\end{equation}
\nomenclature{$E$}{Energy\nomunit{J}}
\nomenclature{$m$}{Mass\nomunit{kg}}
\nomenclature{$c$}{Speed of light\nomunit{m/s}}
\end{document}
this is what I get:

- nomencl.png (13.55 KiB) Viewed 16750 times
What exactly do you want different?
Personally I prefer glossaries for this as it is highly customizable, allows for multiple glossaries and ...
Regards