How to set-up LuaTeX, Microtype, with Minion Pro, Myriad Pro

Hm, I also use Minion Pro and Myriad Pro … this way:

\documentclass[12pt]{scrbook}
\usepackage[english]{babel}
\usepackage{blindtext}
\pdfprotrudechars=2
\pdfadjustspacing=2
\usepackage{fontspec}
\defaultfontfeatures{Ligatures=TeX}
\newfontfeature{Microtype}{protrusion=default;expansion=default;}
\setmainfont[Microtype,Ligatures=TeX,Numbers=OldStyle]{Minion Pro}
\setsansfont[Microtype,Scale=MatchLowercase,Ligatures=TeX,Numbers=OldStyle]{Myriad Pro}
\begin{document}
\blindtext[5]
\end{document}

Than TeX Live 2010 and now 2011.

With the current microtype from TeXlive 2011, you can do the following:

\documentclass{article}
\usepackage{fontspec,microtype}
\defaultfontfeatures{Ligatures=TeX, Scale=MatchLowercase}


\setmainfont[SmallCapsFeatures={LetterSpace=6}, Numbers={Proportional,OldStyle}]{Minion Pro}
\setsansfont[LetterSpace=3, Numbers={Proportional,OldStyle}]{Myriad Pro}


\SetProtrusion
   [ name     = min-eu2 ]
   { encoding = {EU2},
     family   = MinionPro  }
   {
     {,} = {  ,500},
      -  = {  ,500}
   }


\begin{document}
  \hsize 3in

When, while the lovely valley teems with vapour around me, and the meridian sun strikes the upper surface of the impenetrable
foliage of my trees, and but a few stray gleams steal into the inner sanctuary, I throw myself down among the tall grass by the
trickling stream; and, as I lie close to the earth, a thousand unknown plants are noticed by me.

\end{document}

LuaTeX with fontspec uses EU2 encoding internally, so all you need to do is the regular microtype setup with encoding EU2.