GPL clause 2a: How do YOU document your changes?

Clause 2a of the GPL states:

 >   2. You may modify your copy or copies of the Program or any portion
 > of it, thus forming a work based on the Program, and copy and
 > distribute such modifications or work under the terms of Section 1
 > above, provided that you also meet all of these conditions:
 >
 >     a) You must cause the modified files to carry prominent notices
 >     stating that you changed the files and the date of any change.

This clause differs from the practices I have observed in the community.

In particular, it is common to simply include a notice that the program
as a whole has been changed (e.g. in a README) from some "original"
distribution, rather than putting that notice on each modified file.

I've also noticed that it is unusual to find a list of specific changes
with dates on them.

I'm not too concerned about fixing the practices of every project we
contribute to.  Mainline changes are generally managed by the primary
copyright holder who certainly has a special status wrt to the GPL.

I'm more concerned about specialized forks of GPL'd projects which my
company maintains.  A lot of project maintainers are not particularly
concerned with incorporating changes to support embedded real-time
applications.

Do you maintain a fork of a GPL'd program?  If so, what do you do to
comply with this clause?

What do you recommend that we do?  Is an automtically-generated
changelog in each file sufficient?  Is it overkill?