I want to use a manual Bibliography but I need it as a subsection. In order to do this I did:

\documentclass[12pt]{article}

\begin{document}

\section{My Section}

\subsection{References}

\begingroup

\renewcommand{\section}[2]{}%

\begin{thebibliography}{}

\bibitem{notes} John W. Dower {\em Readings compiled for History
21.479.}  1991.

\end{thebibliography}
\endgroup

\end{document}


By doing this, I am hiding the default "References" section title and replacing it with my manual \subsection{References} title. This works great, but the problem I am having right now is that the default "References" title shows up on my Table of Contents when I use \tableofcontents. How can I remove the default title (the one created by \begin{thebibliography}{}) from my Table of Contents?

Without using any packages, you can just remove the \addcontentsline macro's functionality before calling \subsection{References}:

\documentclass[12pt]{article}

\begin{document}
\tableofcontents
\section{My Section}

\begingroup
\renewcommand{\section}[2]{}% Remove functionality of \section
\subsection{References}

\begin{thebibliography}{}
\bibitem{notes} John W. Dower {\em Readings compiled for History
21.479.}  1991.
\end{thebibliography}
\endgroup

\end{document}


You can use the tocvsec2 package to change the tocdepth to 1 just before the subsection (you can restore the value after the bibliography, if needed). I also used the etoolbox package to patch \thebibliography and suppress the default title:

\documentclass{article}
\usepackage{tocvsec2}
\usepackage{etoolbox}

\patchcmd{\thebibliography}{\section*{\refname}}{}{}{}

\begin{document}

\tableofcontents

\section{My Section}

\settocdepth{section}
\subsection{References}
\begin{thebibliography}{}
\bibitem{notes} John W. Dower {\em Readings compiled for History
21.479.}  1991.
\end{thebibliography}
%\settocdepth{subsection}% in case you need this

\end{document}