Footnotes tabularx-environment LaTeX
Probably somebody understands tabularx:-)
The footnote in tabularx is designed to enable page footnotes with the text coming at the end of the page. If you are not seeing the text then most likely you have the table in some other box (such as a float) that inhibits footnotes whether or not they are in a table.
If you want table notes the standard latex way is to put the tabular in a minipage then the footnotes come at the end of the minipage.
Or you might prefer the code in this answer
\footnotetext numbering for many \footnotemark - automatic solution
Your edited MWE works for me giving footnotes:
the file list shows that your MWE loads 166 files, approximately all of them are not needed for this example, so it's too much to ask anyone to debug. I attach my list below. I would start by removing everything you are not using in that example the footnote push/pop from the other answer siunits (and all the l3exp code) in fact as far as I can see your MWE only uses tabularx then most likely you will get footnotes, then just put back the packages you think you need. If the footnotes go, it is a problem with that package.
*File List*
article.cls 2007/10/19 v1.4h Standard LaTeX document class
size11.clo 2007/10/19 v1.4h Standard LaTeX file (size option)
inputenc.sty 2008/03/30 v1.1d Input encoding file
latin1.def 2008/03/30 v1.1d Input encoding file
fontenc.sty
t1enc.def 2005/09/27 v1.99g Standard LaTeX file
geometry.sty 2010/07/13 v5.5 Page Geometry
keyval.sty 1999/03/16 v1.13 key=value parser (DPC)
ifpdf.sty 2010/01/28 v2.1 Provides the ifpdf switch (HO)
ifvtex.sty 2010/03/01 v1.5 Switches for detecting VTeX and its modes (HO)
parskip.sty 2001/04/09 non-zero parskip adjustments
setspace.sty 2000/12/01 6.7 Contributed and Supported LaTeX2e package
amsmath.sty 2000/07/18 v2.13 AMS math features
amstext.sty 2000/06/29 v2.01
amsgen.sty 1999/11/30 v2.0
amsbsy.sty 1999/11/29 v1.2d
amsopn.sty 1999/12/14 v2.01 operator names
amssymb.sty 2009/06/22 v3.00
amsfonts.sty 2009/06/22 v3.00 Basic AMSFonts support
gensymb.sty 2003/07/02 v1.0 (WaS)
babel.sty 2008/07/06 v3.8l The Babel package
english.ldf 2005/03/30 v3.3o English support from the babel system
siunitx.sty 2010/07/15 v2.0n A comprehensive (SI) units package
expl3.sty 2010/07/13 v1982 L3 Experimental code bundle wrapper
l3names.sty 2010/07/11 v1981 L3 Experimental Naming Scheme for TeX Primitiv
es
etex.sty 1998/03/26 v2.0 eTeX basic definition package (PEB)
l3basics.sty 2010/06/07 v1942 L3 Experimental basic definitions
l3expan.sty 2010/06/10 v1948 L3 Experimental Argument Expansion module
l3tl.sty 2010/05/22 v1919 L3 Experimental Token Lists
l3intexpr.sty 2010/06/15 v1957 L3 Integer Expressions
l3quark.sty 2010/03/21 v1853 L3 Experimental Quark Commands
l3seq.sty 2010/03/29 v1879 L3 Experimental sequences and stacks
l3toks.sty 2010/05/25 v1933 L3 Experimental Token Registers
l3int.sty 2010/05/25 v1933 L3 Experimental Integer module
l3prg.sty 2010/03/21 v1853 L3 Experimental control structures
l3clist.sty 2010/03/29 v1878 L3 Experimental comma separated lists
l3token.sty 2010/04/11 v1890 L3 Experimental token investigation and manipu
lation
l3prop.sty 2010/03/21 v1857 L3 Experimental Property Lists
l3msg.sty 2010/03/23 v1866 L3 Experimental LaTeX Messages module
l3io.sty 2010/05/22 v1923 L3 Experimental i/o module
l3skip.sty 2010/05/25 v1933 L3 Experimental skip registers
l3box.sty 2010/05/22 v1919 L3 Experimental Box module
l3keyval.sty 2010/04/11 v1890 L3 Experimental keyval processing
l3keys.sty 2010/05/24 v1931 L3 Experimental key-value support
l3precom.sty 2010/02/09 v1793 L3 Experimental precompilation module
l3xref.sty 2010/02/09 v1786 L3 Experimental cross referencing
l3file.sty 2010/03/21 v1853 L3 Experimental file loading
l3fp.sty 2010/07/08 v1979 L3 Experimental floating-point operations
calc.sty 2007/08/22 v4.3 Infix arithmetic (KKT,FJ)
array.sty 2008/09/09 v2.4c Tabular extension package (FMi)
l3keys2e.sty 2009/08/24 v1494 Parsing LaTeX3 keyvals as LaTeX2e package opti
ons
xparse.sty 2010/05/23 v1927 Generic document command parser
translator.sty 2010/06/12 ver 1.10
translator-language-mappings.tex
graphicx.sty 1999/02/16 v1.0f Enhanced LaTeX Graphics (DPC,SPQR)
graphics.sty 2009/02/05 v1.0o Standard LaTeX Graphics (DPC,SPQR)
trig.sty 1999/03/16 v1.09 sin cos tan (DPC)
graphics.cfg 2010/04/23 v1.9 graphics configuration of TeX Live
pdftex.def 2010/02/14 v0.04n Graphics/color for pdfTeX
tabularx.sty 1999/01/07 v2.07 `tabularx' package (DPC)
booktabs.sty 2005/04/14 v1.61803 publication quality tables
multirow.sty
url.sty 2006/04/12 ver 3.3 Verb mode for urls, etc.
hyperref.sty 2010/06/18 v6.81g Hypertext links for LaTeX
ltxcmds.sty 2010/04/26 v1.7 LaTeX kernel commands for general use (HO)
kvsetkeys.sty 2010/03/01 v1.9 Key value parser (HO)
infwarerr.sty 2010/04/08 v1.3 Providing info/warning/message (HO)
etexcmds.sty 2010/01/28 v1.3 Prefix for e-TeX command names (HO)
pdfescape.sty 2010/03/01 v1.9 Provides hex, PDF name and string conversions
(HO)
pdftexcmds.sty 2010/04/01 v0.9 Utility functions of pdfTeX for LuaTeX (HO)
ifluatex.sty 2010/03/01 v1.3 Provides the ifluatex switch (HO)
ifxetex.sty 2009/01/23 v0.5 Provides ifxetex conditional
hycolor.sty 2009/12/12 v1.6 Color options of hyperref/bookmark (HO)
xcolor-patch.sty 2009/12/12 xcolor patch
letltxmacro.sty 2008/06/24 v1.3 Let assignment for LaTeX macros (HO)
pd1enc.def 2010/06/18 v6.81g Hyperref: PDFDocEncoding definition (HO)
intcalc.sty 2007/09/27 v1.1 Expandable integer calculations (HO)
hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
kvoptions.sty 2010/02/22 v3.7 Keyval support for LaTeX options (HO)
bitset.sty 2007/09/28 v1.0 Data type bit set (HO)
bigintcalc.sty 2011/01/30 v1.2 Expandable big integer calculations (HO)
atbegshi.sty 2010/03/25 v1.12 At begin shipout hook (HO)
hpdftex.def 2010/06/18 v6.81g Hyperref driver for pdfTeX
atveryend.sty 2010/03/24 v1.5 Hooks at very end of document (HO)
rerunfilecheck.sty 2010/03/16 v1.6 Rerun checks for auxiliary files (HO)
uniquecounter.sty 2009/12/18 v1.1 Provides unlimited unique counter (HO)
caption.sty 2010/01/09 v3.1m Customizing captions (AR)
caption3.sty 2010/01/14 v3.1m caption3 kernel (AR)
mhchem.sty 2010/06/16 v3.08 for typesetting chemical formulae
ifthen.sty 2001/05/26 v1.1c Standard LaTeX ifthen package (DPC)
twoopt.sty 2008/08/11 v1.5 Definitions with two optional arguments (HO)
appendix.sty 2009/09/02 v1.2b extra appendix facilities
cite.sty 2009/08/29 v 5.2
fancyhdr.sty
translator-basic-dictionary-English.dict
supp-pdf.mkii
epstopdf-base.sty 2010/02/09 v2.5 Base part for package epstopdf
grfext.sty 2007/09/30 v1.0 Managing graphics extensions (HO)
epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Live
nameref.sty 2010/04/30 v2.40 Cross-referencing by name of section
refcount.sty 2008/08/11 v3.1 Data extraction from references (HO)
gettitlestring.sty 2009/12/18 v1.3 Cleanup title references (HO)
tab77.out
tab77.out
umsa.fd 2009/06/22 v3.00 AMS symbols A
umsb.fd 2009/06/22 v3.00 AMS symbols B
I think this is a good opportunity to pimp out parnotes:
\documentclass[a4paper,11pt]{article}
\usepackage[latin1]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{geometry,parskip,setspace,amsmath,amssymb,amsfonts,gensymb}
\usepackage[english]{babel}
\usepackage[per-mode=symbol]{siunitx}
\usepackage{graphicx,tabularx,booktabs,multirow,url,hyperref}
\usepackage[hang,small,bf]{caption}
\usepackage[version=3]{mhchem}
\usepackage[page,toc]{appendix}
\usepackage[ref]{cite}
\usepackage{fancyhdr}
\usepackage[roman]{parnotes}
%
% This will go in the next version
%
\makeatletter
\def\parnoteclear{%
\gdef\PN@text{}%
\parnotereset
}
\makeatother
% ---------- New Commands ----------
\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
\newcolumntype{C}{>{\centering\arraybackslash}X}
\newcolumntype{L}{>{\raggedright\arraybackslash}X}
\begin{document}
\begin{table}[!h]
\centering
\caption{Characteristics of the most common desalination processes \cite{ref1} \label{tab:desalination-properties}}
\begin{tabularx}{1\textwidth}{l l L L}
\toprule
\parnoteclear % tabularx will otherwise add each note thrice
Property & Reverse Osmosis & MSF\parnote{For large MSF plants} & MED \\
\midrule
El.\parnote{El. = electrical} energy consumption [\si{\kilo\watt\per\cubic\metre}] & $6.5-12$ & $4-6$ \ref{ref1} & $4.5-12.5$ \\
Th.\parnote{Th. = thermal} energy consumption [\si{\kilo\watt\per\cubic\meter}] & & $55-120$ \ref{ref1} & \\
Plant cost & High & Medium & Low \\
Product quality & Medium\parnote{Energy dependent} & High & High \\
Feed pretreatment & High & Medium & Low \\
Maintenance & High & Low & Low \\
\bottomrule
\end{tabularx}
\parnotes
\end{table}
\begin{thebibliography}{9}
\bibitem{ref1} Some reference
\end{thebibliography}
\end{document}
