inset plot with pgfplots

Depending on what exactly you're trying to highlight with the inset, the spy library might be useful for you. It creates an insert with a magnified part of a TikZ picture.

In order to use the axis cs: coordinate system for specifying which part to magnify, you have to create a coordinate node in the axis, as axis cs: is not available inside the \spy command:

\documentclass{article}
\usepackage{pgfplots}
\usetikzlibrary{spy}
\begin{document}

\begin{tikzpicture}[spy using outlines={rectangle, magnification=3,connect spies}]
\begin{axis}[grid=major,no markers,domain=-5:5,enlargelimits=false]
\addplot {x^2};
\addplot {x^3};

\coordinate (spypoint) at (axis cs:0,0);
\coordinate (spyviewer) at (axis cs:0.5,-90);
\spy[width=6cm,height=1cm] on (spypoint) in node [fill=white] at (spyviewer);
\end{axis}

\end{tikzpicture}

\end{document}

You could use the xshift, and yshift keys:

\documentclass{article}
\usepackage{pgfplots}

\begin{document}

\begin{tikzpicture}
 \begin{axis}[xshift=.5\textwidth,yshift=2cm,width=0.45\textwidth]
  %small plot
 \end{axis}
 \begin{axis}[width=\textwidth]
  %large plot
 \end{axis}
\end{tikzpicture}

\end{document}

You can place an inset relatively to the main plot by doing

\documentclass{standalone}
\usepackage{pgfplots}
\begin{document}
\begin{tikzpicture}[remember picture]
    \begin{axis}[width=\textwidth]
    %large plot
    \addplot {x^3};
    \coordinate (insetPosition) at (rel axis cs:0.95,0.05);
    \end{axis}
    \begin{axis}[at={(insetPosition)},anchor={outer south east},footnotesize]
    %small plot
    \addplot {2*x};
    \end{axis}
\end{tikzpicture}
\end{document}

which then gives you

This automatically shifts to make space for the subsets axis descriptions too. Occasionally one might want to place such a subset at a fixed coordinate, in which case you only need to exchange the definition of insetPosition to

\coordinate (insetPosition) at (axis cs:5:-140);

to achieve this effect.