You said,
Is it possible to customise the colours for the desktop theme and window appearance in Pangolin 12.04 as it was possible in Narwhal?
I assume, you are referring to the customization window in the theme in Natty Narwhal and previous distributions. Since, Gnome 3 is released, those easy customization options are removed default.
But, the good news is, the corresponding keys in gconf and hence dconf is available still now. So, you can change those keys using dconf-editor (dconf-editor or gsettings should be used instead of gconf, since settings are migrating to dconf).
I've tested in Narwhal and found the corresponding keys, the path is /org/gnome/desktop/interface and
the keys are as follows:
bg_color - It refers to the window color. This corresponds to left color selection in Windows row i.e 1st row in Narwhal.
fg_color - This controls the text colors in windows, menus, title bars etc. This is the right side color selection in Windows row (It does not change the text color in input boxes, nautilus folder pane etc, text in editors etc).
base_color - This controls the background colors in input boxes, nautilus folder pane, editor's background, search bar, address bar in browsers etc. Corresponds to the left color selection in Input boxes row in Narwhal.
text_color - This controls the text colors (foreground colors) in the above settings, such as input boxes, nautilus folder pane, editor's text, search bar, address bar's text etc. Corresponds to the right color selection box in Input boxes row in Narwhal.
selected_bg_color - This controls the background color i,e the color of any selections, when you select with your mouse etc. Corresponds to the Selected Items row's left-most settings in Narwhal.
selected_fg_color - This controls the text colors withing selection. Corresponds to the Selected Items row's right settings.
tooltip_bg_color - This I think self-explanatory. It controls the background colors of a tooltip. Corresponds to the Tooltips row's first settings.
tooltip_fg_color - This controls the tool tip text color. Corresponds to the right settings in Tooltips row in Narwhal
How to set those colors:
You can easily set those colors in dconf-editor. Install it via terminal with the command:
sudo apt-get install dconf-tools
or via Software Center 
Now, Open dconf-editor by typing the name in dash. To do so, Press Super and type dconf-editor and Click on the icon.
Go to the path org -> gnome -> desktop -> interface and select gtk-color-scheme and input value there. Don't forget to put a ; after each key-value pair. For example, If you want to change the window color(bg_color) and window text color(fg_color) with some values, the line should be like this:
bg_color:#2f568f;fg_color:#000000;
Generate color value:
To generate color value, you can use the Appearance Window in System Settings. To bring it. Right Click on Desktop -> Choose Change Desktop Background and in the Window, click the little color box below the big Monitor image. There you can see a custom color box. click there.
Alternatively, you can use agave color generator. It is a very convenient and tiny tool to generate color value. Install it with terminal using the commmand:
sudo apt-get install agave
or using Software center
Type agave in the dash to open it after pressing Super
Changing window border color:
Changing window border's color of default Ambiance and Radiance themes aren't supported. Because, those themes use images as window borders. If you really want to have the ability to change the window border, I suggest you to use old colorable window borders such as Crux, Esco, Human etc.
Some are included in the default Ubuntu installation. You can use those by using Ubuntu-tweak.
After installation, open it by Pressing Super and typing "Ubuntu tweak" in the dash. Then go to Tweaks -> Themes and then change Window Theme.
Best Answer
Firstly, the GTKParasite application does not handle themes at all. It might be useful to detect if the misbehaving application is a GTK application at all and determine the class of the editor widget. In Windows-speak, it is the Spy++ of GTK.
Changing the editor color affects the lot of applications that directly use the GtkText widget (and to some extent the GtkSourceView widget at the root of syntax coloring editors like gedit and geany).
Applications like Firefox and *Office are not real GTK applications, they have their own cross-platform widget set that render GTK decorations but do not have the association to the real text editor class.
Bluefish is a real GTK app but seems to implement its own text editor widget since it does not look like GtkSourceView or SciTe at all. You will probably find a lot of applications that jump to the conclusion that all text background should be white, and changing them globally won't be possible without some per-application-tweaking.