You can achieve the partial ToC using the titletoc package and its \startcontents, \printcontents, \stopcontents commands. A little example, showing the partial ToC for a section and the active hyperlinks:
\documentclass{article}
\usepackage{titletoc}
\usepackage{hyperref}
\newcommand\innercontentsname[1]{%
Contents for section~\ref{#1}}
\let\oldthesubsection\thesubsection
\begin{document}
\section{A regular section}
\subsection{Regular subsection one}
\subsection{Regular subsection two}
\section{Section with inner units and partial ToC}
\label{sec:ptoc}
\renewcommand\thesubsection{\Alph{subsection}}
\startcontents[inner]
\printcontents[inner]{}{1}{\subsection*{\innercontentsname{sec:ptoc}}}
\subsection{Inner special subsection one}
\subsection{Inner special subsection two}
\subsubsection{Inner special subsubsection one}
\subsubsection{Inner special subsubsection two}
\subsection{Inner special subsection three}
\stopcontents[inner]
\renewcommand\thesubsection{\oldthesubsection}
\section{Another regular section}
\subsection{Regular subsection one}
\subsection{Regular subsection two}
\end{document}

In a comment to the question, it has been requested that the inner subsections shouldn't be included in the general table of contents; this can be achieved by using \startcontents, \printcontents, \resumecontents to print the general table of contents:
\documentclass{article}
\usepackage{titletoc}
\usepackage{hyperref}
\newcommand\innercontentsname[1]{%
Contents for section~\ref{#1}}
\let\oldthesubsection\thesubsection
\begin{document}
\startcontents
\printcontents{}{1}{\section*{\contentsname}}
\section{A regular section}
\subsection{Regular subsection one}
\subsection{Regular subsection two}
\section{Section with inner units and partial ToC}
\label{sec:ptoc}
\renewcommand\thesubsection{\Alph{subsection}}
\stopcontents[default]
\startcontents[inner]
\printcontents[inner]{}{1}{\subsection*{\innercontentsname{sec:ptoc}}}
\subsection{Inner special subsection one}
\subsection{Inner special subsection two}
\subsubsection{Inner special subsubsection one}
\subsubsection{Inner special subsubsection two}
\subsection{Inner special subsection three}
\stopcontents[inner]
\renewcommand\thesubsection{\oldthesubsection}
\resumecontents
\section{Another regular section}
\subsection{Regular subsection one}
\subsection{Regular subsection two}
\end{document}

\noindent \textbf{\hypertarget{isecone}{InnerSubSectionOne}} \\. The inner section are rather short and they'd rather disturb/distract on the main table of contents. I was about to add alphabetic counting manually, but thought there has to be a lightweight solution to this. The problem is for me even installing a counter is kind of...well..hard. – Jan 22 '14 at 20:33