Variable-width horizontal rules with \cline intrude cell text

Both problems are related. \cline has to support several \clines in a row, e.g.:

\documentclass{article}
\begin{document}
  \begin{tabular}{*{5}{c}}
    1 & 2 & 3 & 4 & 5\\
    \cline{1-1}\cline{3-3}\cline{5-5}
    A & B & C & D & E
  \end{tabular}
\end{document}

Therefore \cline cannot move down like \hline, the definition of \cline is (latex.ltx):

\def\cline#1{\@cline#1\@nil}
\def\@cline#1-#2\@nil{%
  \omit
  \@multicnt#1%
  \advance\@multispan\m@ne
  \ifnum\@multicnt=\@ne\@firstofone{&\omit}\fi
  \@multicnt#2%
  \advance\@multicnt-#1%
  \advance\@multispan\@ne
  \leaders\hrule\@height\arrayrulewidth\hfill
  \cr
  \noalign{\vskip-\arrayrulewidth}}

In the last step \cline moves back to the original vertical position.

But the vertical space for the line can be added after the \clines, e.g.:

\cline{...}\cline{...}\noalign{\vskip\arrayrulewidth}

Applied to your example, it can be added to macro \whline. This fixes also the problem with \cellcolor:

\documentclass{article}
\usepackage{array}
\usepackage{colortbl}

\begin{document}

\newcolumntype{I}{!{\vrule width 3pt}}
\newlength\savedwidth

\newcommand\whline[1]{%
  \noalign{%
    \global\savedwidth\arrayrulewidth\global\arrayrulewidth 6pt%
  }%
  \cline{#1}%
  \noalign{\vskip\arrayrulewidth}%
  \noalign{\global\arrayrulewidth\savedwidth}%
}
\begin{tabular}{|cIc|c|}\hline
 A & B & C \\ \hline
 X & \cellcolor{red}Y & Z \\ \whline{1-3}
 \cellcolor{green}100 & 10 & 1 \\ \hline
\end{tabular}

\end{document}

Here is Heiko's example using cals package as an alternative:

\documentclass{article}
\usepackage{xcolor}
\usepackage{cals}
\begin{document}
\begin{calstable}
\colwidths{{10mm}{10mm}{10mm}}
\makeatletter
\brow
\cell{A}
\def\cals@borderL{2pt}\cell{B}\let\cals@borderL=\relax
\cell{C}
\erow
\brow
\def\cals@borderB{3pt}
\cell{X}
\def\cals@borderL{2pt}\def\cals@bgcolor{red}
 \cell{Y}\let\cals@borderL=\relax\def\cals@bgcolor{}
\cell{Z}
\erow
\let\cals@borderB=\relax
\brow
\def\cals@bgcolor{green}\cell{100}\def\cals@bgcolor{}
\def\cals@borderL{2pt}\cell{10}\let\cals@borderL=\relax
\cell{1}
\erow
\end{calstable}
\end{document}