To add your nomenclature, bibliography and index to the table of contents you have the choice between
using built-in options of the corresponding packages, i.e., using
\usepackage[intoc]{nomencl},\printbibliography[heading=bibintoc]and\usepackage[totoc]{idxlayout}, ordoing this manually by adding
\cleardoublepage \phantomsection \addcontentsline{toc}{chapter}{xxx}before
\printnomenclature,\printbibliographyand\printindex.
Both methods give the same visual output.
Method 1 seems to be preferable because it is much cleaner code, you don't have to use the same three lines of method 2 several times and you don't have to manually type the heading name in the addcontentsline.
However, if you're using hyperref, the links in the toc point to the first line after the corresponding heading (i.e., the heading itself is not visible). Compare it to the link to a standard chapter which points to a position quite a bit above the heading. The same is true for method 2.
Is this behavior intentional? If so, why? Can i somehow use method 1 and still get links as in method 2?
Method 1 (only for nomenclature, the same holds for bibliography and index):
\documentclass{scrreprt}
\usepackage[intoc]{nomencl}
\usepackage{hyperref}
\makenomenclature
\begin{document}
\tableofcontents
\nomenclature{$T$}{test}
\chapter{Test}
\printnomenclature
\end{document}
Method 2 (only for nomenclature, the same holds for bibliography and index):
\documentclass{scrreprt}
\usepackage{nomencl}
\usepackage{hyperref}
\makenomenclature
\begin{document}
\tableofcontents
\nomenclature{$T$}{test}
\chapter{Test}
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{Nomenclature}
\printnomenclature
\end{document}

hyperrefdo you use? – Marco Daniel Apr 9 '12 at 9:13