beamer can't automatically wrap the mini frames into a new line if they don't fit into a single one. Instead, a new line is started for each subsection when using with the miniframes theme:

Unfortunately this doesn't work for the Darmstadt theme you are using. The reason for this is that Darmstadt loads the outer theme smoothbars, which is very similar to the miniframes theme, but installs smooth shaded transitions between the header and the content. However, it also uses beamer's compress option to get all the mini frames into a single line, so using multiple subsections doesn't work here. Removing this option is not a good idea, though, because the shading is hard-coded into the theme, so the header can't change its height automatically and will overflow if you use multiple lines for the mini frames:

So the only thing you can do is to replace the smoothbars outer theme with miniframes (producing the headline shown in the first image):
\documentclass{beamer}
\usetheme{Darmstadt}
\useoutertheme{miniframes}
\makeatletter
\beamer@compressfalse
\makeatother
\begin{document}
\section{Section 1}
\subsection{Subsection 1}
\frame{}\frame{}\frame{}
\subsection{Subsection 2}
\frame{}\frame{}\frame{}\frame{}
\subsection{Subsection 3}
\frame{}
\end{document}
Like this, you can wrap the mini frames into several lines by using multiple subsections, as shown in the example code.
miniframesand not withsmoothbars, the difference is thatminiframeshave no shading. Are you interested in that? – tohecz Jan 23 '12 at 13:01