Update april 2013
The bug has been fixed with pgfplots version 1.8 (requires \pgfplotsset{compat=1.8}).
When I try to add the axes labels to this code, I get a division by zero error. I think the error is responsive to the choice of the unit vectors directions (see after).
\documentclass{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=1.7} % *EDIT*: this improves scale uniformly.
\begin{document}
\begin{tikzpicture}
\begin{axis}[axis lines=center,
% *EDIT*: this here respects your choice of unit vectors.
% scale uniformly computes one common scaling factor
% and chooses limits such that the image fulfills the
% prescribed width/height as best as possible.
x={(-0.3535cm,-0.3535cm)}, y={(1cm,0cm)}, z={(0cm,1cm)},
scale mode=scale uniformly,
xlabel={$x$}, ylabel={$y$}, zlabel={$z$},
]
\addplot3 coordinates {(0,0,0) (0.5,-0.5,0.8)};
\end{axis}
\end{tikzpicture}
\end{document}

Now look at this code with a different choice of unit vectors. The axes labels are drawn (I get no error), but far away from their axis and overlapped. Moreover, the actual width is about 5 cm and not 10 cm as it should be (scale only axis won't help here).
\documentclass[tikz]{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=1.7} % *EDIT*: this improves scale uniformly.
\begin{document}
\begin{tikzpicture}
\begin{axis}[width=10cm,
axis lines=center,
xmin=0, xmax=1, ymin=-1, ymax=1, zmin=0, zmax=1,
% *EDIT*: this here respects your choice of unit vectors.
% scale uniformly computes one common scaling factor
% and chooses limits such that the image fulfills the
% prescribed width/height as best as possible.
x={(0.94cm,-0.34cm)}, y={(0.766cm,0.643cm)}, z={(0cm,1cm)},
scale mode=scale uniformly,
xlabel={$x$}, ylabel={$y$}, zlabel={$z$},
]
\addplot3 coordinates {(0,0,0) (0.5,-0.5,0.8)};
\end{axis}
\end{tikzpicture}
\end{document}


\node at (axis cs: 0.85,0,0) {$x$}; \node at (axis cs: 0,0.30,0) {$y$}; \node at (axis cs: 0,0,0.85) {$z$};. – Peter Grill Nov 27 '12 at 10:02widthandheightkeys have no effect, because the dimensions of the plot are already determined by the axis ranges and the unit vectors. – Jake Nov 27 '12 at 10:15