Theming or changing colors for Nautilus?

Yes. You can create a custom nautilus.rc (for GTK+ 2.x) or nautilus.css (for GTK+ 3.x). Unfortunately I do not have a link or instructions on exactly how to theme it, but there are a few themes out there that have these files inside (such as Ambiance and Radiance), and if you take a look at how their definitions for Nautilus are structured, you should be able to work it out pretty easily.

Since nautilus is gtk, it will use the same theme as the rest of the gnome applications, so you can search for a theme than you like.

The only thing I can think if you don't want to change the gtk theme in the rest of apps, onlyfor nautilus, is create an script than launches nautilus whit a diferent theming:

For example, I use ultimate edition theme in all my gnome, but I don't like how it looks in firefox, so I made a script called "firefox" and put it inside my $HOME/.scripts directory. The script contains just this:

#!/bin/bash
env GTK2_RC_FILES=/usr/share/themes/New\ Wave\ Dark\ Menus/gtk-2.0/gtkrc /usr/bin/firefox "$@"

Now you'll have to make a script called nautilus, and change the word firefox in the script for the route to nautilus executable. And of course change the "New\ Dark\ Menus for the name of a theme you like for nautilus and you have installed in /usr/share/themes

One thing, if the name of the theme contains spaces, you have to put \ before each space so the script recognize the route.

Wish it helps

EDIT:

I forgot to say. If you want to launch that script manually you'll need only to call it, in the directory where it is like this: First you allow it to run (just needed the first time:

chmod +x nautilus

Run it:

./nautilus

But if you want to run nautilus with this script by default, you'll need to create a folder where to put your scripts, save it inside and define that folder as your personal script path:

mkdir .scripts

Copy the nautilus script inside and give it permisions with

chmod +x .scripts/nautilus

Set $HOME/.scripts as a PATH:

echo "PATH=$HOME/.scripts:$PATH" >> .bash_profile

This way, every time nautilus is started it will be started for your personal script.