Code for http://tex.stackexchange.com/a/120529/14066

color-ligatures.lua

documentdata                  = documentdata or { }
documentdata.color_ligatures  = { }
local color_ligatures         = documentdata.color_ligatures

color_ligatures.color         = { r = 0xee/255,
                                  g = 0x31/255,
                                  b = 0x09/255, }

local stringformat            = string.format

local copynode                = node.copy
local insertnodeafter         = node.insert_after
local insertnodebefore        = node.insert_before
local newnode                 = node.new
local traversenodes           = node.traverse
local traversenodetype        = node.traverse_id

local nodecodes               = nodes.nodecodes

local glyph_t                 = nodecodes.glyph
local disc_t                  = nodecodes.disc
local hlist_t                 = nodecodes.hlist
local whatsit_t               = nodecodes.whatsit
local pdf_literal_t           = 8

local get_color = function ()
  local color   = color_ligatures.color
  local push    = stringformat ("%.3g %.3g %.3g rg",
                                color.r,
                                color.g,
                                color.b)
  local pop     = "0 g"
  return push, pop
end

local pdf_literal = newnode(whatsit_t, pdf_literal_t)

local cbk = function (hd)
  local pushcolor, popcolor = get_color()
  local push, pop = copynode(pdf_literal), copynode(pdf_literal)
  push.mode, push.data = 1, pushcolor
  pop.mode,  pop.data  = 1, popcolor

  for line in traversenodetype(hlist_t, hd) do
    local hlist = line.list
    for n in traversenodes(hlist) do
      --- locate ligatures
      if  n.id == glyph_t and n.components then
        --- surround with color literals
        local before, after = copynode(push), copynode(pop)
        hlist = insertnodebefore(hlist, n, before)
        hlist = insertnodeafter (hlist, n, after)
      elseif n.id == disc_t then
        local replace = n.replace
        if replace and replace.components then
          local before, after = copynode(push), copynode(pop)
          hlist = insertnodebefore(hlist, n, before)
          hlist = insertnodeafter (hlist, n, after)
        end
      end
    end
  end
  return hd
end

local hook    = "post_linebreak_filter"
local active  = false

color_ligatures.enable = function ()
  if active == false then
    luatexbase.add_to_callback (hook, cbk, "my.color_ligatures")
    active = true
  end
end
  
color_ligatures.disable = function ()
  if active == true then
    luatexbase.remove_from_callback (hook, "my.color_ligatures")
    active = false
  end
end

color_ligatures.set_color = function (r, g, b)
  color_ligatures.color = { r = (tonumber(r, 16) or 0) / 255,
                            g = (tonumber(g, 16) or 0) / 255,
                            b = (tonumber(b, 16) or 0) / 255, }
end

color-ligatures.tex

%% http://tex.stackexchange.com/q/120397/14066
\input luaotfload.sty
%% uncomment this for node mode (default in luaotfload):
%\font\mainfont="file:Iwona-Regular.otf" at 30pt \mainfont

\directlua{dofile "color-ligatures.lua"}

\def\startcolorligatures{%
  \directlua{documentdata.color_ligatures.enable()}%
}

\def\stopcolorligatures{%
  \endgraf %% paragraph-based callback
  \directlua{documentdata.color_ligatures.disable()}%
}

\def\setligaturecolor#1#2#3{%%-> rgb values
  \directlua{documentdata.color_ligatures.set_color("#1", "#2", "#3")}
}

before a ff b ffi c ffl d

\startcolorligatures
during a ff b ffi c ffl d

\setligaturecolor{0}{0}{bb}
different color a ff b ffi c ffl d
\stopcolorligatures

after a ff b ffi c ffl d

\bye

Absolutely amazing.