You could alter the legend of the second plot "by hand" by using \addlegendimage{<plot options>} \addlegendentry{<plot title>} after the second plot. You can access the <plot options> of the first plot by assigning a \label{<name>} to it and using the key /pgfplots/refstyle=<name> in your \addlegendimage command:

Another option would be to label the plots directly. Since pgfplots version 1.5.1, you can place nodes a specified length along the plot by including a node [pos=<fraction>] {} in the \addplot command.

Depending on how you're going to use the graph, you could also consider colouring the axis to match the plots. This will be problematic if you need to print the document in black and white, but in a presentation, this might be more elegant than forcing the audience's eyes from the plot line to the legend and then to the y axes in order to match plot and axis.
I've defined a style y axis style=<colour> that simultaneously sets the colour for y axis line style, y tick style, yticklabel style and ylabel style, so you can just call y axis style=red!75!black to set all the elements belonging to the y axis to that colour.

One legend for both axes
\documentclass{article}
% UNITS
\usepackage{siunitx}
\sisetup{per=slash, load=abbr}
% GRAPHICS
\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{width=7cm,compat=1.3}
\begin{document}
\begin{tikzpicture}
\pgfplotsset{
scale only axis,
scaled x ticks=base 10:3,
xmin=0, xmax=0.06
}
\begin{axis}[
axis y line*=left,
ymin=0, ymax=80,
xlabel=$Q/\si{\m\cubed\per\s}$,
ylabel=$H/\si{\m}$,
]
\addplot[smooth,mark=x,blue]
coordinates{
(0,68.6)
(0.0148,72)
(0.0295,68.6)
(0.0441,53.4)
(0.059,22.8)
}; \label{Hplot}
\end{axis}
\begin{axis}[
axis y line*=right,
axis x line=none,
ymin=0, ymax=100,
ylabel=$\eta/\si{\percent}$
]
\addlegendimage{/pgfplots/refstyle=Hplot}\addlegendentry{$H$}
\addplot[smooth,mark=*,red]
coordinates{
(0,0)
(0.0148,48)
(0.0295,66)
(0.0441,66)
(0.059,45.0)
}; \addlegendentry{$\eta$}
\end{axis}
\end{tikzpicture}
\end{document}
Plots directly labeled
\documentclass{article}
% UNITS
\usepackage{siunitx}
\sisetup{per=slash, load=abbr}
% GRAPHICS
\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{width=7cm,compat=newest}
\begin{document}
\begin{tikzpicture}
\pgfplotsset{
scale only axis,
scaled x ticks=base 10:3,
xmin=0, xmax=0.06
}
\begin{axis}[
axis y line*=left,
ymin=0, ymax=80,
xlabel=$Q/\si{\m\cubed\per\s}$,
ylabel=$H/\si{\m}$
]
\addplot[smooth,mark=x,blue]
coordinates{
(0,68.6)
(0.0148,72)
(0.0295,68.6)
(0.0441,53.4)
(0.059,22.8)
} node [pos=0.04,anchor=north, text=black] {$H$}; \label{Hplot}
\end{axis}
\begin{axis}[
axis y line*=right,
axis x line=none,
ymin=0, ymax=100,
ylabel=$\eta/\si{\percent}$
]
\addplot[smooth,mark=*,red]
coordinates{
(0,0)
(0.0148,48)
(0.0295,66)
(0.0441,66)
(0.059,45.0)
} node [pos=0.9,anchor=south west, text=black] {$\eta$};
\end{axis}
\end{tikzpicture}
\end{document}
Axis colours match plot colours
\documentclass{article}
% UNITS
\usepackage{siunitx}
\sisetup{per=slash, load=abbr}
% GRAPHICS
\usepackage{tikz}
\usepackage{pgfplots}
\pgfplotsset{width=7cm,compat=newest}
\begin{document}
\begin{tikzpicture}
\pgfplotsset{
scale only axis,
scaled x ticks=base 10:3,
xmin=0, xmax=0.06,
y axis style/.style={
yticklabel style=#1,
ylabel style=#1,
y axis line style=#1,
ytick style=#1
}
}
\begin{axis}[
axis y line*=left,
y axis style=blue!75!black,
ymin=0, ymax=80,
xlabel=$Q/\si{\m\cubed\per\s}$,
ylabel=$H/\si{\m}$
]
\addplot[smooth,mark=x,blue]
coordinates{
(0,68.6)
(0.0148,72)
(0.0295,68.6)
(0.0441,53.4)
(0.059,22.8)
};
\end{axis}
\begin{axis}[
axis y line*=right,
axis x line=none,
ymin=0, ymax=100,
ylabel=$\eta/\si{\percent}$,
y axis style=red!75!black
]
\addplot[smooth,mark=*,red]
coordinates{
(0,0)
(0.0148,48)
(0.0295,66)
(0.0441,66)
(0.059,45.0)
};
\end{axis}
\end{tikzpicture}
\end{document}
\label{plot:one}immediately after the first\addplot ...;and then\ref{plot:one}in the caption. – cmhughes Jan 29 '12 at 21:23pgfplotsmanual, and still, nothing. All I get is an unresolved-reference error. – Ricardo Jan 30 '12 at 02:44legend pos=north westto the firstaxisenvironment, for example, so that\etais in the top left, andHis in the top right – cmhughes Jan 30 '12 at 04:12articleclass, but my document is atufte-handoutclass, that places the captions in the margin. In thearticleclass it works as expected, but in thetufte-handouteven when I tried protecting the\refas recommended in the pgfmanual, it still did not work. I like the idea of placing each serie's legend close to it's axis. I'll try it. – Ricardo Jan 30 '12 at 19:47