The size option file of the class (svjour3.clo) defines the font sizes \normalsize, \small and \footnotesize so that they contain two \ifs. E.g. :
\renewcommand\normalsize{%
\if@twocolumn
\@setfontsize\normalsize\@xpt{12.5pt}%
\else
\if@smallext
\@setfontsize\normalsize\@xpt\@xiipt
\else
\@setfontsize\normalsize{9.5pt}{11.5pt}%
\fi
\fi
\abovedisplayskip=3 mm plus6pt minus 4pt
\belowdisplayskip=3 mm plus6pt minus 4pt
\abovedisplayshortskip=0.0 mm plus6pt
\belowdisplayshortskip=2 mm plus4pt minus 4pt
\let\@listi\@listI}
That's rather unusual and it obviously confuse microtype. I don't understand why they put the if-switches in the font definitions - I doubt that they want to switch the sizes inside a document. Perhaps they only want to avoid to have to copy the \abovedisplayskip part around.
You will have to rearrange the definitions:
\documentclass{svjour3}
\makeatletter
\if@twocolumn
\renewcommand\normalsize{%
\@setfontsize\normalsize\@xpt{12.5pt}%
\abovedisplayskip=3 mm plus6pt minus 4pt
\belowdisplayskip=3 mm plus6pt minus 4pt
\abovedisplayshortskip=0.0 mm plus6pt
\belowdisplayshortskip=2 mm plus4pt minus 4pt
\let\@listi\@listI}%
\renewcommand\small{%
\@setfontsize\small{8.5pt}\@xpt
\abovedisplayskip 8.5\p@ \@plus3\p@ \@minus4\p@
\abovedisplayshortskip \z@ \@plus2\p@
\belowdisplayshortskip 4\p@ \@plus2\p@ \@minus2\p@
\def\@listi{\leftmargin\leftmargini
\parsep 0\p@ \@plus1\p@ \@minus\p@
\topsep 4\p@ \@plus2\p@ \@minus4\p@
\itemsep0\p@}%
\belowdisplayskip \abovedisplayskip}
\else
\if@smallext
\renewcommand\normalsize{%
\@setfontsize\normalsize\@xpt\@xiipt
\abovedisplayskip=3 mm plus6pt minus 4pt
\belowdisplayskip=3 mm plus6pt minus 4pt
\abovedisplayshortskip=0.0 mm plus6pt
\belowdisplayshortskip=2 mm plus4pt minus 4pt
\let\@listi\@listI}%
\renewcommand\small{%
\@setfontsize\small\@viiipt{9.5pt}%
\abovedisplayskip 8.5\p@ \@plus3\p@ \@minus4\p@
\abovedisplayshortskip \z@ \@plus2\p@
\belowdisplayshortskip 4\p@ \@plus2\p@ \@minus2\p@
\def\@listi{\leftmargin\leftmargini
\parsep 0\p@ \@plus1\p@ \@minus\p@
\topsep 4\p@ \@plus2\p@ \@minus4\p@
\itemsep0\p@}%
\belowdisplayskip \abovedisplayskip}
\else
\renewcommand\normalsize{%
\@setfontsize\normalsize{9.5pt}{11.5pt}%
\abovedisplayskip=3 mm plus6pt minus 4pt
\belowdisplayskip=3 mm plus6pt minus 4pt
\abovedisplayshortskip=0.0 mm plus6pt
\belowdisplayshortskip=2 mm plus4pt minus 4pt
\let\@listi\@listI}%
\renewcommand\small{%
\@setfontsize\small\@viiipt{9.25pt}%
\abovedisplayskip 8.5\p@ \@plus3\p@ \@minus4\p@
\abovedisplayshortskip \z@ \@plus2\p@
\belowdisplayshortskip 4\p@ \@plus2\p@ \@minus2\p@
\def\@listi{\leftmargin\leftmargini
\parsep 0\p@ \@plus1\p@ \@minus\p@
\topsep 4\p@ \@plus2\p@ \@minus4\p@
\itemsep0\p@}%
\belowdisplayskip \abovedisplayskip}
\fi
\fi
\let\footnotesize\small
\makeatother
\usepackage{microtype}
\begin{document}
abc
\end{document}