One possibility would be to declare your background-image as a pgfimage with \pgfdeclareimage command and insert it in a modified \insertslideintonotes command.
Something like:
\documentclass[notes]{beamer}
\usepackage{blindtext}
\newcommand{\newbackground}[1]{%
\setbeamertemplate{background canvas}{%
\includegraphics[width=\paperwidth,height=\paperheight]{#1}}
\pgfdeclareimage[width=\paperwidth,height=\paperheight]{background}{#1}
}
\makeatletter
\renewcommand{\insertslideintonotes}[1]{{%
\begin{pgfpicture}{0cm}{0cm}{#1\paperwidth}{#1\paperheight}
\begin{pgflowlevelscope}{\pgftransformscale{#1}}%
{\pgftransformshift{\pgfpointorigin}\pgftext[left,bottom]{\pgfuseimage{background}}}
\color{normal text.fg}
{\pgftransformshift{\pgfpoint{\beamer@origlmargin}{\footheight}}\pgftext[left,bottom]{\copy\beamer@frameboxcopy}}
\end{pgflowlevelscope}
\end{pgfpicture}%
}}
\makeatother
\setbeamertemplate{background canvas}{\includegraphics[width=\paperwidth,height=\paperheight]{lion_in_masai_mara.jpg}}
\setbeameroption{show notes}
\begin{document}
\newbackground{lion_in_masai_mara}
\begin{frame}
\blindtext
\end{frame}
\note{A lion in the topright minislide :(}
\newbackground{lion_in_masai_mara_2}
\begin{frame}
\blindtext
\end{frame}
\note{Another lion in the topright minislide :(}
\end{document}

Improved version
What's new?
1.- It's possible to use \newbackground{} to go back to default (empty) background.
It uses \@ifmtarg command (see, for example, Werner's answer to How to check if a macro value is empty or will not create text with plain TeX conditionals?)
2.- Scoping background: {\newbackground{figure}\begin{frame}....\end{frame}\notes{...}} works.
3.- Smiles fixed ;-)
What's changed?
It uses \setbeamertemplate{background} instead of \setbeamertemplate{background canvas} because default background template definition is empty while background canvas is not. Therefore it's easier to use \ifbeamertemplateempty condition without having to affect default background canvas.
New code and examples:
\documentclass[notes]{beamer}
\usepackage{ifmtarg}
\usepackage{blindtext}
\makeatletter
\newcommand{\newbackground}[1]{%
\@ifmtarg{#1}{%
\setbeamertemplate{background}[default]
}{
\setbeamertemplate{background}{\includegraphics[width=\paperwidth,height=\paperheight]{#1}}
\pgfdeclareimage[width=\paperwidth,height=\paperheight]{background}{#1}
}%
}
%
\renewcommand{\insertslideintonotes}[1]{{%
\begin{pgfpicture}{0cm}{0cm}{#1\paperwidth}{#1\paperheight}
\begin{pgflowlevelscope}{\pgftransformscale{#1}}%
\ifbeamertemplateempty{background}{%
\color{normal text.bg}
\pgfpathrectangle{\pgfpointorigin}{\pgfpoint{\paperwidth}{\paperheight}}
\pgfusepath{fill}
}{%
\pgftransformshift{\pgfpointorigin}\pgftext[left,bottom]{\pgfuseimage{background}}
}
\color{normal text.fg}
{\pgftransformshift{\pgfpoint{\beamer@origlmargin}{\footheight}}\pgftext[left,bottom]{\copy\beamer@frameboxcopy}}
\end{pgflowlevelscope}
\end{pgfpicture}%
}}
\makeatother
\setbeameroption{show notes}
%\setbeamertemplate{background canvas}{}
\begin{document}
{
\newbackground{lion_in_masai_mara}
\begin{frame}
\blindtext
\end{frame}
\note[itemize]
{\item A lion in the topright minislide :)
\item Only for this frame. Next one should be empty.}
}
\begin{frame}
\blindtext
\end{frame}
\note[itemize]{
\item No lion in the topright minislide :))
\item As I told you.
\item Next one will have a different lion.
}
\newbackground{lion_in_masai_mara_2}
\begin{frame}
\blindtext
\end{frame}
\note[itemize]{
\item Another lion in the topright minislide :)))
\item Used \texttt{\textbackslash{}newbackground\{lion\_in\_masai\_mara\_2\}} }
\newbackground{}
\begin{frame}
\blindtext
\end{frame}
\note[itemize]{
\item No lion in the topright minislide :))
\item Made empty with \texttt{\textbackslash{}newbackground\{\}} }
\end{document}

ifand I'll try do do it better. – Ignasi Jun 20 '13 at 13:30\graphicspathfor the thumbnail backgrounds so the backgrounds better be in a consistent place (I hardcoded my path into the\pgfdeclareimagecall which is ugly but works). Related: http://sourceforge.net/p/pgf/feature-requests/41/ – Christian Jan 31 '15 at 22:42