One of my biggest gripes with SharePoint is the difficulty in
branding application or layout pages. These are the pages that no
matter how much you tweak your master page, remain blue.
EXAMPLE:
here is my nice branded site

I want to upload a document, so i click upload document and get
thrown back to this ugly page:

ouch!
I discussed one possible option for the user profile pages in an
article series: How to
customize the user information page (part 3)
But that is a lot of work if you are going to do it for a large
number of pages - it may be plausible if there are half a dozen but
in a collaboration portal scenario there are dozens of these
pages.
So what are the options currently available....
Customize the files in the Layouts folder
This is actually the recommended approach by MSFT. Its very
simple - take a backup and then modify away.
The obvious disadvanatge is when you are hosting more than one
site on the same server - the changes affect all sites in your
farm. Oh and any service pack/hotifx could overwrite any of your
chnages.
Create a custom Layouts folder
This is a little better than the last method. You take a copy of
the layouts directory and update IIS to point to the copy. Now all
site collections in a single web app will share any modifications
which is pretty acceptable. Your files can still be overwritten and
you may get some strange behaviour for anything hardcoded to the
layouts dir.
Check this Knowledge
byte article for more info on these 2 methods.
SuperBranding
So this definately comes closest to an acceptable solution. Its
a CodePlex
project that has been put together by the legendary Ted
Pattison. The way it works is by running an HTTP Module that
intercepts page requestsa and overrides the preinit method to
attach a custom mater page. Now we have full flexibilty and MSFT
won't overwrite our customizations.
The upload page with superbranding:

That is a million times better!!!