Here is another approach: at first the point where the cloud should start is marked and then the could is positioned starting from that position. The command \mycallout is overlay-aware therefore allows you some customization.
Notice that you can position a cloud regardless having marked a point, but doing it allows the pointer to be vertically aligned with respect the sentence (the last cloud is not).
\documentclass[slidestop,compress,mathserif,12pt,xcolor=dvipsnames]{beamer}
\graphicspath{{images/}}
\definecolor{LHCblue}{RGB}{4, 114, 255}
\usecolortheme[named=LHCblue]{structure}
\usepackage[bars]{beamerthemetree} % Beamer theme v 2.2
\usepackage{kerkis}
\usepackage{multimedia}
\usepackage{subfigure}
\mode<presentation>
%frame
\newcommand*\oldmacro{}%
\let\oldmacro\insertshorttitle%
\renewcommand*\insertshorttitle{%
\oldmacro\hfill%
\insertframenumber\,}%/\,\inserttotalframenumber
\setbeamertemplate{footline}[frame number]
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\setbeamercovered{higly dynamic}
\usetheme[watermark=ntua-logo.jpg]{Ilmenau} % Beamer theme v 3.0
\useoutertheme[subsection=true]{smoothbars}%Beamer Outer Theme-circles on top
\useinnertheme{circles} %rectangle bullet points instead of circle ones
\usepackage{beamerthemebars}
\setbeamercolor{navigation symbols dimmed}{fg=red!80!black}
\setbeamercolor{navigation symbols}{fg=red!80!black}
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\title[July 2012 H4 Test Beam\hspace{3cm} Stony Brook, NYC]{July 2012 H4 Test Beam}
\author[Stamatopoulos N. Athanasios\hspace{2.5cm}{athanasios.stamatopoulos@cern.ch}] {Stamatopoulos N. Athanasios}
\institute{NTUA/CERN}
\logo{%
\makebox[0.99\paperwidth]{%
\includegraphics[width=1cm,keepaspectratio]{logopolito}%
\hfill%
\includegraphics[width=1cm,keepaspectratio]{ntua-logo}%
}%
}
\usepackage{textpos}
\usepackage{tikz}
\usetikzlibrary{%
calc,%
fadings,%
shadings%
}
\usetikzlibrary{arrows,decorations,shapes}
%\usepackage{enumitem}
%\usepackage{paralist}
\usepackage{xparse}
\tikzset{
invisible/.style={opacity=0},
visible on/.style={alt=#1{}{invisible}},
alt/.code args={<#1>#2#3}{%
\alt<#1>{\pgfkeysalso{#2}}{\pgfkeysalso{#3}} % \pgfkeysalso doesn't change the path
},
}
\NewDocumentCommand{\mycallout}{r<> m m}{%
\tikz[remember picture, overlay]\node[visible on=<#1>,align=center,draw,shading=ball,text=white,cloud callout,cloud puffs=17,cloud puff arc=140,callout pointer segments=3,anchor=pointer,callout relative pointer={(200:2cm)}, aspect =2.5,scale=0.5]
at (#2) {#3};
}
\newcommand{\tikzmark}[1]{\tikz[overlay,remember picture,baseline=-0.5ex] \node (#1) {};}
\begin{document}
\begin{frame}
\begin{itemize}
\item<1-> XY Resistive MM
\item<2-> Manufactured by Rui de Oliveira \tikzmark{this point}\quad
\mycallout<3>{this point}{Thank you Rui!}
\item<4-> Another sentence with a callout \tikzmark{bla} \mycallout<5>{bla}{Bla bla bla}
\end{itemize}
\vfill
Another text. \mycallout<6>{0,0}{My text}
\vfill
\end{frame}
\end{document}
Result:

Percusse suggested to comment the warning deriving from your code:
Class beamer Warning: slidestop'' is obsolete. Uset'' instead on input lin
e 343.
Class beamer Warning: mathserif'' is obsolete. Use font themeserif'' with
option ``onlymath'' on input line 343.
You can avoid them by means of substituting the first two lines in your code:
\documentclass[t,compress,12pt,xcolor=dvipsnames,]{beamer}
\usefonttheme[onlymath]{serif}
Notice that also the snakes library is obsolete: you can use decorations although in the current example is not needed.
The equivalent xparse-free solution:
\documentclass[t,compress,12pt,xcolor=dvipsnames,]{beamer}
\usefonttheme[onlymath]{serif}
\usepackage{lmodern}
\graphicspath{{images/}}
\definecolor{LHCblue}{RGB}{4, 114, 255}
\usecolortheme[named=LHCblue]{structure}
\usepackage[bars]{beamerthemetree} % Beamer theme v 2.2
\usepackage{kerkis}
\usepackage{multimedia}
\usepackage{subfigure}
\mode<presentation>
%frame
\newcommand*\oldmacro{}%
\let\oldmacro\insertshorttitle%
\renewcommand*\insertshorttitle{%
\oldmacro\hfill%
\insertframenumber\,}%/\,\inserttotalframenumber
\setbeamertemplate{footline}[frame number]
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\setbeamercovered{higly dynamic}
\usetheme[watermark=ntua-logo.jpg]{Ilmenau} % Beamer theme v 3.0
\useoutertheme[subsection=true]{smoothbars}%Beamer Outer Theme-circles on top
\useinnertheme{circles} %rectangle bullet points instead of circle ones
\usepackage{beamerthemebars}
\setbeamercolor{navigation symbols dimmed}{fg=red!80!black}
\setbeamercolor{navigation symbols}{fg=red!80!black}
%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\title[July 2012 H4 Test Beam\hspace{3cm} Stony Brook, NYC]{July 2012 H4 Test Beam}
\author[Stamatopoulos N. Athanasios\hspace{2.5cm}{athanasios.stamatopoulos@cern.ch}] {Stamatopoulos N. Athanasios}
\institute{NTUA/CERN}
\logo{%
\makebox[0.99\paperwidth]{%
\includegraphics[width=1cm,keepaspectratio]{logopolito}%
\hfill%
\includegraphics[width=1cm,keepaspectratio]{ntua-logo}%
}%
}
\usepackage{textpos}
\usepackage{tikz}
\usetikzlibrary{%
calc,%
fadings,%
shadings%
}
\usetikzlibrary{arrows,decorations,shapes}
%\usepackage{enumitem}
%\usepackage{paralist}
\tikzset{
invisible/.style={opacity=0},
visible on/.style={alt=#1{}{invisible}},
alt/.code args={<#1>#2#3}{%
\alt<#1>{\pgfkeysalso{#2}}{\pgfkeysalso{#3}} % \pgfkeysalso doesn't change the path
},
}
\newcommand{\mycallout}[3]{%
\tikz[remember picture, overlay]\node[visible on=<#1>,align=center,draw,shading=ball,text=white,cloud callout,cloud puffs=17,cloud puff arc=140,callout pointer segments=3,anchor=pointer,callout relative pointer={(200:2cm)}, aspect =2.5,scale=0.5]
at (#2) {#3};
}
\newcommand{\tikzmark}[1]{\tikz[overlay,remember picture,baseline=-0.5ex] \node (#1) {};}
\begin{document}
\begin{frame}
\begin{itemize}
\item<1-> XY Resistive MM
\item<2-> Manufactured by Rui de Oliveira \tikzmark{this point}\quad
\mycallout{3}{this point}{Thank you Rui!}
\item<4-> Another sentence with a callout \tikzmark{bla} \mycallout{5}{bla}{Bla bla bla}
\end{itemize}
\vfill
Another text. \mycallout{6}{0,0}{My text}
\vfill
\end{frame}
\end{document}
newcommand. It is really fancy! Thank you both soooo much!!! – Thanos Sep 27 '12 at 13:19