longtable has two settings for the headers of the table: \endfirsthead and \endhead. The contents of \endfirsthead will be saved in the save box \LT@firsthead and the contents of \endhead in \LT@head. If the box \LT@firsthead is empty, longtable uses the contents of \LT@head. The same procedure will be used for the footer. In the same way I defined a \endsecondhead
\def\endsecondhead{\LT@end@hd@ft\LT@secondhead}
To use this command I have to define a new save box which will be set only on the second page.
\newbox\LT@secondhead
To make sure that only on the second page this box will be used I have to manipulate the output of longtable. Therefore I use a simple \ifvoid clause.
\ifvoid\LT@secondhead
\copy\LT@head\nobreak
\else
\box\LT@secondhead\nobreak
\fi
\ifvoid tests whether the save box \LT@secondhead is empty or not. If you set a second head, the box will be printed by \box. This command prints the box and clears the box. So on the next page the test above is true. In this way you make sure that when no second head is defined the \endhead will be used.
To allow for more than three different headings you must define new save boxes and extend the test.
\documentclass{article}
\usepackage{forloop,longtable}
\newcounter{count}
\setcounter{count}{1}
\makeatletter
\newbox\LT@secondhead
\def\endsecondhead{\LT@end@hd@ft\LT@secondhead}
\def\LT@output{%
\ifnum\outputpenalty <-\@Mi
\ifnum\outputpenalty > -\LT@end@pen
\LT@err{floats and marginpars not allowed in a longtable}\@ehc
\else
\setbox\z@\vbox{\unvbox\@cclv}%
\ifdim \ht\LT@lastfoot>\ht\LT@foot
\dimen@\pagegoal
\advance\dimen@-\ht\LT@lastfoot
\ifdim\dimen@<\ht\z@
\setbox\@cclv\vbox{\unvbox\z@\copy\LT@foot\vss}%
\@makecol
\@outputpage
\ifvoid\LT@secondhead
\setbox\z@\vbox{\box\LT@head}%
\else
\setbox\z@\vbox{\box\LT@secondhead}%
\fi
\fi
\fi
\global\@colroom\@colht
\global\vsize\@colht
\vbox
{\unvbox\z@\box\ifvoid\LT@lastfoot\LT@foot\else\LT@lastfoot\fi}%
\fi
\else
\setbox\@cclv\vbox{\unvbox\@cclv\copy\LT@foot\vss}%
\@makecol
\@outputpage
\global\vsize\@colroom
\ifvoid\LT@secondhead
\copy\LT@head\nobreak
\else
\box\LT@secondhead\nobreak
\fi
\fi}
\makeatother
\begin{document}
\listoftables
\section{section}
\begin{longtable}{c}
\caption{foo}\\\stepcounter{table}\endfirsthead
\caption{foo bar}\\\stepcounter{table}\endsecondhead
\caption{bar}\\\endhead
\whiledo{\value{count} < 100}{\stepcounter{count}
\arabic{count} \\}
\end{longtable}
\end{document}