That was a quick two years.. but in that time I believe I've perfected the time/date-naming of photos taken off my digital cameras. And the best tool I've found so far to do it with turns out to be one available free: Microsoft's
Windows Live Photo Gallery.
With it you can import photos from a camera and prepend the date each photo was taken*, say
2010-05-30 Himalayan Mountains 001.jpg and place them in your folders where ever you choose. [*The date is the Exif time/date taken that cameras record. NB Keep it current!]
I use a belt-and-braces method of first choosing a Month folder, e.g. 2010-05 (C:\Users\Public\Pictures\2010-05), and then specifying that for the import. You change it once a month, at the start of each. You can specify all photos from your camera's card or choose to import just some at a time, or just new ones. You can auto-delete them upon import but I've decided to keep them all on my cards and save the cards, full. They're much cheaper than a roll of film and they're a good safety backup.
Set the 'Import to' folder as above, set Folder name as '(None)' (it's already chosen), and set File name as 'Date Taken + Name' to get the 'himalaya' structure. Choose your ticks to taste.
While that method may not be flexible enough for you - getting a good description for each photo or group of, I then use the indispensable tool Total Commander, with the Exif Tool add-on. With TC and its Multi-Rename Tool (Ctrl-M) I can change parts of files' filenames. Or, if it's a really tricky set, BRU comes in to do the job.
And what's especially good about TC with the Exif add-on is that you can rename existing camera files -
retrospectively - since they'll probably contain embedded Exif data: e.g. 'Date Original' and 'Time Original'. You can create your own columns with which to view Exif data in the file manager. I haven't seen this capability in BRU; please tell me if I've missed it.
Edit1: Ahh, I reminded myself of the title of this thread and I see that I may be speaking in reverse purposes. As for resetting file timestamps - I have decided to ignore the dates and times that file managers like Windows Explorer, Xplorer2, Total Commander etc report; they're a lost cause. They're file system parameters and are as changeable as the breeze.

I advise that you look elsewhere for timestamps that are more controllable; that's why I now rely upon filenames and Exif data.
Edit2: In conclusion, with regard to WiLiPhGallery, I find that since the one constant in human experience is time, it helps to have files stored in time-related folders - but there's more: it doesn't matter - WLPG uses that time structure as a convenience but then lets you tag photos supremely easily. Singles, multiples, drag'n'drop, include all, remove, not yet tagged, file info and photo edit, make panoramas, email resized attachments, view by tag(s), print, burn, publish, movies, etc. Indeed, you can edit or slide the times taken if it's wrong on your camera. And the tags are embedded in the files' Exif data, so you don't have to depend on the one program.