Coloring combining characters without changing color of a base character

To exemplify Caramdir's comment, the following minimal example produces base and combining characters of different color when compiled with XeLaTeX or LuaLaTeX:

documentclass{minimal}
usepackage{fontspec}
usepackage{xcolor}
setmainfont[Script=Hebrew]{Arial}
begin{document}
textcolor{red}{א}textcolor{blue}{֣}textcolor{green}{֚}בtextcolor{blue}{ָ}textcolor{green}{ג}֦דtextcolor{green}{֘}
end{document}

One possible solution would be to exploit the babel Hebrew support. Recall that cp1255, for instance, has the following declaration:

DeclareInputText{200}{hebqamats}

Using renewcommand, you could redefine hebqamats to include coloring commands prior to the insertion of the actual glyph. In order to avoid infinite loops, you'd of course have to refer to the glyph by its cp1255 character code (200).

For completeness sake, here is an answer using ConTeXt's font colour schemes feature (using Arabic, but should apply to any scripts):

First write a font “goodies” file containing categories of glyphs names (glyph name are font dependant, so you've to check the font you are using) that should share the same colour (it is just a lua script):

-- save as 'amiri.lfg'
return {
    name = "Amiri",
    version = "1.00",
    comment = "Goodies that complement the Amiri font.",
    author = "Khaled Hosny",
    colorschemes = {
        default = {
            [1] = { -- category 1
                "uni064E", "uni064B",
            },
            [2] = { -- category 2
                "uni064F", "uni064C",
            },
            [3] = { -- category 3, etc.
                "uni0650", "uni064D",
            },
        }
    }
}

Update: With ConTeXt 2012.03.02 it is now possible to use Unicode character numbers instead of glyph names, so the the lfg file will not be font dependant (using glyph names is still good to access un-encoded glyphs, which is font dependant by definition).

-- save as 'amiri.lfg'
return {
    name = "Amiri",
    version = "1.00",
    comment = "Goodies that complement the Amiri font.",
    author = "Khaled Hosny",
    colorschemes = {
        default = {
            [1] = { -- category 1
                0x064E, 0x064B,
            },
            [2] = { -- category 2
                0x064F, 0x064C,
            },
            [3] = { -- category 3, etc.
                0x0650, 0x064D,
            }, 
        }
    }
}

Then you can use it from your ConTeXt document, using usual font and colour conventions:

% overload ‘arabic‘ font feature set to load the goodies
definefontfeature[arabic][arabic]
                  [goodies=amiri,       % name of the goodies file
                   colorscheme=default] % name of the scheme we defined

% define color scheme 1, categories 1, 2 and 3
definecolor[colorscheme:1:1][r=1]
definecolor[colorscheme:1:2][g=1]
definecolor[colorscheme:1:3][b=1]

% color scheme 2
definecolor[colorscheme:2:1][c=.55]
definecolor[colorscheme:2:2][m=.55]
definecolor[colorscheme:2:3][y=.55]

setupalign[r2l]

starttext
% load the font
definedfont[name:amiri*arabic at 36pt]

setfontcolorscheme[1]
ضَرَبَ ضُرِبَ ضَرْبًا

setfontcolorscheme[2]
ضَرَبَ ضُرِبَ ضَرْبًا
stoptext

I will here sum up a solution hinted at in a mailing list post linked to in the OP's question (the link in the question is dead; working link here: XeTeX mailing list link, 2007 July, 6989).

It is possible to achieve this in XeLaTeX without the use of any additional packages if you have access to a font editor software. However, there is some manual work involved and it is probably too tedious if you have more than a handful of cases.

The trick is to make a duplicate of the base letter and make it invisible, then use negative kerning to overlay the invisible base + colored mark with the normal (black) base.

The procedure is as follows (exact steps depend on the font editor):

1. In the font editor, load your font and make a duplicate of the base letter. Make sure that the duplicate preserves the exact metrics (width and sidebearings), and also keeps the anchors in the same positions, but delete the stroke. Assign the duplicate a code in the PUA or define it as a stylistic alternative to make it accessible in a layout engine / word processor.
2. Still inside the font editor, note the x-height and the width of the base character.
3. Export the font and install it on your system.
4. In the XeLaTeX-file, type something like this: {color{red} INVISIBLE BASE + MARK}kern-1.42ex NORMAL BASE. You will need to adjust the value for kerning, which you can calculate from the width of the base / x-height.

I have successfully used this procedure with the font editor Glyphs and XeLaTeX to make colored bases with black diacritics (so the inverse of the OP's question).