If you use oldstyle digits for section numbers, you should use them for all “nonmath” numbers, that is, all numbers not used in their proper mathematical sense, such as page numbers in addition to section numbers.
Some font families provide oldstyle digits, but not Computer Modern other than with the clumsy \oldstyle command. However, you can use cfr-lm that uses the Latin Modern fonts, which are almost identical to Computer Modern. With cleveref it becomes easy adding the § mark in front of the number in references. For the section number in titles, just modify \@seccntformat. I would use oldstyle digits also for equation numbers, as they are just markers, but in the following code there's a line that can change them to lining digits.
\documentclass{article}
\usepackage[
rm={oldstyle=true},
]{cfr-lm}
\usepackage{amsmath}
\makeatletter
\renewcommand\@seccntformat[1]{\S\csname the#1\endcsname\quad}
% Uncomment the following line for lining digits in equation numbers
%\renewcommand\maketag@@@[1]{\hbox{\m@th\normalfont\lstyle#1}}
\makeatother
\usepackage{cleveref}
\crefformat{section}{\S#2#1#3}
\begin{document}
\section{Introduction}\label{sec:intro}
Here we talk about something, with an equation
\begin{equation}\label{eq:good}
1+1=2
\end{equation}
Here's a ref to the present section, which is \cref{sec:intro}, and
one to equation~\eqref{eq:good}.
\end{document}
What are the advantages in doing this? The \thesection command doesn't get touched, remaining fully expandable and usable with packages such as refcount. The cleveref package is very powerful and recommendable for getting uniform references across the document. Finally, the call to cfr-lm can be changed to
\usepackage[osf,sc]{mathpazo}
to use Palatino with oldstyle digits, without any other change to your document.

\oldstylenums{1234567890}to see the effect. Then try something like\renewcommand{\thesection}{\S\oldstylenums{\arabic{section}}.}– karlkoeller Aug 28 '13 at 16:50