Haven't I just said that MOST PROGRAMS DON'T SAVE THESE THINGS properly?
You are wrong.
The vast majority of programs save to AppData and a few programs in ProgramData. Very rarely are those saved in registry.
You need to manually reconfigure or manually import/export them. that indeed takes some time. But if you know how it doesn't take a week.
Photoshop for example saves this crap in the Registry, so bye bye once you reinstall Windows ::- )
http://forums.adobe.com/thread/462065
10 seconds google search, bam!
As I said, I make my images freshly after install of programs & OS & settings. So there is no cleaning to do, there is no junk ::- ).
Yes there IS junk.
Even the greatest experts install shitty junk software without realizing it or out of necessity on occasion.
If you ever installed foxit reader or adope reader then your system is tainted until reformat. (recommendation, use SumatraPDF).
Low quality anti-virus solutions like norton?
Did you upgrade your video card and switched between AMD and nVidia? uh-oh!
Did you make the horrible mistake of buying a creative audio card and saddled with their OS ruining drivers?
What is that? You installed MS Virtual Studio 2005/2008? Well too bad it makes irreversible OS changes and you have 2010 or with to switch to a FOSS alternative.
Furthermore, WTF!
You ranted about photoshop settings being uncopyable and now you claim to do a "clean install, install programs, configure settings, and image" process?...
Do you honestly expect me to believe you NEVER EVER add anything to your photoshop? that you can make an image in jan 1st 2010 and then just happily revert to it today without losing your precious PS scripts, settings, and customizations?
Or are you thinking that superficial junk like the location of panels which takes literally under 1 minute combined to make all changes for PS? I hope you don't and refer to more complex stuff like scripts, color palettes, etc.
please tell me how you would migrate Photoshop's panel layouts and preferences.

That stuff takes LITERALLY under a minute to redo. I have done it a dozen times. But I am giving you the benefit of the doubt and assuming "preferences" to include actual valuable custom stuff you made. Here are the instructions...
http://forums.adobe.com/thread/462065
10 seconds google search, bam!
And, if you use it, also tell me the same thing about Microsoft Word and Outlook (where does it store its e-mail accounts? And no, not the messages themselves, I know those reside in the PST).
Why would I use that POS?
And it stores it in appdata
http://email.about.com/od/outlooktips/ss/find_ol_data.htm
PS. An important thing about my system is that I am always prepared, ahead of time, to do a reinstall... I set up automatic backups for anything that needs it. If windows fails to load I don't panic about my lost program settings, I reinstall windows and just plop them back in.
If I reverted to an image made right after a clean install, I would lose months of settings, and gained a little junk.
If I reverted to a recent image I would lose a little but gain much more junk and issues.