I have just finished my thesis, which is ready for defence and print!
It consists of tex subfiles which are added to a main file. The thesis is written in Greek. I used roman numbering for the first chapters(abstract in Greek and English, aknowledgements in Greek and English, Contents). The problem is that the page numbering illustrated in table of contents uses "greek" roman style instead of real roman(please see attached image, red color). However in the real document, page numbering is correct.
The second problem is that files in roman numbering(abstractGR, abstractEN, aknowledgementsGR, aknowledgementsEN) inherit toc chapter heading(green round box in image). How can this be fixed? I made a try by using
\chapter[Abstract]*{Abstract}
or
\chapter*[Abstract]{Abstract}
but it didn't work. In the first case I got an * for chapter name and in the second case a [.

Because of the subfiles I am giving you a link to a folder that contains .tex files and images. The main file is main.tex.
I am just adding the main file's code in case there is something obviously wrong.
\documentclass[11pt,a4paper]{book}
\usepackage[english,greek]{babel}
\setcounter{secnumdepth}{3}
\usepackage[iso-8859-7]{inputenc}
\usepackage{kerkis}
\renewcommand\chaptername{Κεφάλαιο}
\renewcommand\bibname{Βιβλιογραφία}
%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
\usepackage{tocloft}
\makeatletter
\newcommand*{\tocwithouttitle}{\@starttoc{toc}}
\makeatother
%--------------------------------------------------------------------------------
\makeatletter
\newcommand*{\lofwithouttitle}{\@starttoc{lof}}
\makeatother
%--------------------------------------------------------------------------------
\makeatletter
\newcommand*{\lotwithouttitle}{\@starttoc{lot}}
\makeatother
%--------------------------------------------------------------------------------
%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
\renewcommand{\cftsecleader}{\cftdotfill{\cftdotsep}}
\begin{document}
%~~~~~~~~~~~~~~~~~~~~~~~Front-Page~~~~~~~~~~~~~~~~~~~~~~~~~~
\begin{titlepage}
Εξώφυλλο
\end{titlepage}
\pagenumbering{roman}
\textcolor{Darkblue}{\chapter*{\contentsname}}
\markboth{\MakeUppercase{\contentsname}}{\MakeUppercase{\contentsname}}
\textcolor{Darkblue}{\tocwithouttitle}
\addcontentsline{toc}{chapter}{Περιεχόμενα}
\newpage
\subfile{abstractGR.tex}
\addcontentsline{toc}{chapter}{Περίληψη}
\subfile{abstractEN.tex}
\addcontentsline{toc}{chapter}{\eng{Abstract}}
\subfile{aknowledgementsGR.tex}
\addcontentsline{toc}{chapter}{Ευχαριστίες}
\subfile{aknowledgementsEN.tex}
\addcontentsline{toc}{chapter}{\eng{Aknowledgements}}
\textcolor{Darkblue}{\chapter*{Κατάλογος Σχημάτων}}
\markboth{\MakeUppercase{Κατάλογος Σχημάτων}}{\MakeUppercase{Κατάλογος Σχημάτων}}
\textcolor{Darkblue}{\lofwithouttitle}
\addcontentsline{toc}{chapter}{Κατάλογος Σχημάτων}
\newpage
\textcolor{Darkblue}{\chapter*{Κατάλογος Πινάκων}}
\markboth{\MakeUppercase{Κατάλογος Πινάκων}}{\MakeUppercase{Κατάλογος Πινάκων}}
\textcolor{Darkblue}{\lotwithouttitle}
\addcontentsline{toc}{chapter}{Κατάλογος Πινάκων}
\newpage
\pagenumbering{arabic}
\subfile{introductionGR.tex}
\subfile{chapter1.tex}
\subfile{chapter2.tex}
\subfile{chapter3.tex}
\subfile{chapter4.tex}
\subfile{chapter5.tex}
\subfile{chapter6.tex}
\subfile{appendix.tex}
\clearpage
\addcontentsline{toc}{chapter}{Βιβλιογραφία}
\selectlanguage{english}
\bibliographystyle{plain}
\bibliography{test}
\end{document}
It's not a working example, however an experienced user could see my mistake, hopefully.
.zipfile. I'm already at 70MiB and running. :( It's quite difficult that somebody can help you in this way. – egreg Oct 15 '12 at 19:59