I have a main text column with margin a line separation of 1.05 (\setstretch{1.05}), and margin texts generated with a tighter line separation with the following macro:
\newcommand{\mnote}[1]{\marginpar{\raggedright\textsf{\footnotesize{%
\textsf{\footnotesize{%
\begin{spacing}{1.025}%
#1%
\end{spacing}%
}}}}}}%
This results in the following output, where the margin paragraph is not properly algined with the first line of the paragraph of the adjacent main text:
misaligned margin note http://dl.dropbox.com/u/19252957/mnote.png
This is kind of a tough problem to solve. Does someone have any suggestions?

marginnote, which places margin notes on the current line. The macro\marginnoteprovides an optional argument for the vertical adjustment (and the package itself has options regarding this). – Speravir May 16 '12 at 19:51