PSTricks uses \psrunit when drawing \pscircle.

\documentclass[tikz,border=12pt]{standalone}
\newlength\runit
\runit=1cm
\edef\Radius#1{#1\runit}
\begin{document}
\begin{tikzpicture}[x=3cm,y=2cm]
\draw[fill=red] (0,0) circle (\Radius{2});
\draw (-2,-2) rectangle (2,2);
\end{tikzpicture}
\end{document}
Note: declaring the radial unit globally gives you an advantage where you can change all the unit of circle radii in one place.
We can also declare a new key so that we can access this radial unit easier.
\documentclass[tikz,border=12pt]{standalone}
\makeatletter
\newlength\tikz@runit
\tikzset{
r/.code=\pgfmathsetlength\tikz@runit{#1},
r=+1cm, % setting a default value
r radius/.style={radius={(#1)*\tikz@runit}},
xr radius/.style={x radius={(#1)*\tikz@runit}},
yr radius/.style={y radius={(#1)*\tikz@runit}}
}
\makeatother
\begin{document}
\begin{tikzpicture}[x=3cm,y=2cm]
\fill[fill=red] (0,0) circle [r radius=1+1];
\fill[fill=green] (-1,1) circle [xr radius=1+3/4, yr radius=1-1/3]
(1,1) circle [xr radius=1+3/4, yr radius=1-1/3];
\draw (-2,-2) rectangle (2,2);
\end{tikzpicture}
\end{document}

\psrunit(radial unit). – kiss my armpit Apr 12 '13 at 14:08pgfplotschanges the internalx/ycoordinate system too): How to draw on axis from pgfplots? – Qrrbrbirlbel Apr 12 '13 at 16:55