Adding box filled with color and placing large text inside it

You have a problem with xcolor. You need to use the option dvipsnames to use the color MidnightBlue. You don't need to load color because xcolor loads color. pgfplots loads tikz and you need to load xcolor before pgfplots.

You need to compile twice the next code. I used tikz to place a ablack rectangle on the first page.

%!TEX TS-program = xelatex
%!TEX encoding = UTF-8 Unicode   
  % DOCUMENT LAYOUT
\documentclass[10pt, a4paper]{article}
\usepackage[left=5cm,right=2.5cm,top=5cm,bottom=3cm]{geometry}
\usepackage{fontspec}
\usepackage{marvosym}
\usepackage{wasysym}
% DOCUMENT LAYOUT
\setlength\parindent{0cm}
\usepackage[libertine={Ligatures=TeX,Numbers=OldStyle}]{libertineotf}
%\setsansfont{Segoe UI} 
\usepackage[dvipsnames]{xcolor} 
% FONTS
\usepackage{xunicode}
\usepackage{xltxtra}
\defaultfontfeatures{Mapping=tex-text}
\usepackage{pgfplots}

\usepackage{eso-pic}

% ---- CUSTOM COMMANDS
\chardef\&="E050
\newcommand{\html}[1]{\href{#1}{\scriptsize\textsc{[html]}}}
\newcommand{\pdf}[1]{\href{#1}{\scriptsize\textsc{[pdf]}}}
\newcommand{\doi}[1]{\href{#1}{\scriptsize\textsc{[doi]}}}
% ---- MARGIN YEARS
\usepackage{marginnote}
\newcommand{\amper{}}{\chardef\amper="E0BD }
\newcommand{\sides}[1]{\marginnote{\color{MidnightBlue}\sffamily #1}}
%\newcommand{\years}[1]{\marginnote{\footnotesize #1}}
%\renewcommand*{\raggedleftmarginnote}{}
\setlength{\marginparsep}{0.5cm}
\reversemarginpar

% HEADINGS
\usepackage{sectsty} 
\usepackage[normalem]{ulem} 
\sectionfont{\mdseries\upshape\Large}
\subsectionfont{\mdseries\scshape\normalsize} 
\subsubsectionfont{\mdseries\upshape\large}
\usepackage{lipsum}
%\usepackage{tikz}
% PDF SETUP
\usepackage[bookmarks, colorlinks, breaklinks, 
    pdftitle={Here there},
    pdfauthor={My name},
    pdfproducer={}
]{hyperref}  
\hypersetup{linkcolor=blue,citecolor=blue,filecolor=black,urlcolor=MidnightBlue}
% DOCUMENT 


\begin{document}
  \thispagestyle{empty} 
  \begin{tikzpicture}[remember picture,overlay]
  \node[anchor=north west,minimum width=21cm,minimum height=8cm,fill=black,text=white] (RB) at (current page.north west){\Huge TITLE};
\node[text=white,text width=4cm,anchor=north west] at ([shift={(3cm,2cm)}]RB.south west){\emph{Petit texte afin de tester la métode. Petit texte afin de tester la métode. Petit texte afin de tester la métode.}};
\end{tikzpicture}

\vspace*{10cm}
\lipsum[1]
\newpage 
{\LARGE Effect of aspect ratio and others on others and ourselves}\\[3pt]
\textit{Me myself \& You}. Corr. author : \href{mailto:[email protected]}{\textit{[email protected]}}\\
\textit{Department of Mechanical Engineering.}\\[0.5cm]
{\large \bf Abstract}\\[4pt]
\lipsum[25]
{\section*{Introduction}}
\sides{I am hoping to create some proper paper using this template when i do my masters.}
\lipsum
\sides{How does a para look with this on sides. For a moment i thought it is gone}
\lipsum

%\vspace{1cm}
\vfill{}
%\hrulefill

\end{document} 

You can use fancyhdr to place a \colorbox in the header:

\documentclass[10pt, a4paper]{article}
\usepackage[left=5cm,right=2.5cm,top=5cm,bottom=3cm,headheight=22pt]{geometry}% http://ctan.org/pkg/geometry
\usepackage{xcolor}% http://ctan.org/pkg/xcolor
\usepackage{lipsum}% http://ctan.org/pkg/lipsum
\usepackage{fancyhdr}% http://ctan.org/pkg/fancyhdr
\fancypagestyle{unique}{%
  \renewcommand{\headrulewidth}{0pt}% No header rule
  \fancyhf{}% Clear header/footer
  \fancyfoot[C]{\thepage}%
  \fancyhead[C]{%
    \colorbox{black}{\parbox{\dimexpr\textwidth-2\fboxsep}{%
      \color{white}\LARGE Effect of aspect ratio and others on others and ourselves}}%
  }%
}
\begin{document}

\thispagestyle{unique}
\lipsum[1-10]

\end{document}

You can, of course, modify the unique page style to your liking. I've only duplicated the plain page style and added your required header.

Modifications to the header could include stretching the box to span outside the margin. Here's a quick view on the header changes to incorporate it:

\fancypagestyle{unique}{%
  \fancyhf{}% Clear header/footer
  \renewcommand{\headrulewidth}{0pt}% No header rule
  \fancyfoot[C]{\thepage}%
  \fancyhead[C]{%
    \makebox[\textwidth]{%
      \colorbox{black}{\parbox{\dimexpr\textwidth+50pt-2\fboxsep}{%
        \color{white}\LARGE Effect of aspect ratio and others on others and ourselves}}%
  }}%
}

The above header change pushes the coloured box outward (left and right) by 25 points. It accomplishes this by placing a 50pt overset coloured box inside a centred \textwidth box. This avoids LaTeX complaining about an overfull \hbox spanning more than \textwidth.