[The following is more ‘FYI’ than a real answer.]
I agree with other commenters that the space depends on house style (I hope there's little argument that the punctuation is usually desirable).
The breqn package allows the space before equation punctuation to be configurable. With this package (which is compatible with amsmath), you write
\begin{dmath}
y=f(x)
\end{dmath},
where
\begin{dmath}
x=3
\end{dmath}.
Note the equation punctuation in the source is placed after the environments close. When typeset, the punctuation is moved inside the equation, and the space inserted before it is defined by default to be a \thinspace; it can be changed by redefining
\newcommand\eqpunct[1]{\thinspace#1}
I prefer this small space as opposed to setting the punctuation naturally to emphasise that the punctuation is definitely not part of the mathematical expression. Note you could even remove all equation punctuation entirely (which might be appropriate, say, for seminar slides) by writing
\renewcommand\eqpunct[1]{}
and this wouldn't require changing any of the source of your mathematics.