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In the process of upgrading Drupal sites to the latest version 6.3, I have come across a configuration difference between version 6 and previous versions.

Where before I used to put contributed modules and themes into the modules and themes folders, now they should reside under the sites\all\modules and sites\all\themes folders.

So now this makes an upgrade quite a bit easier.

Here is our process

1. For version 6 sites, check the available updates for any other module and theme updates that are required. Log into the site www.website.com/user as administrator.
2. Ensure back up is complete of both home directory and database
3. Go to admin settings, Site configuration, and site maintenance and put site into offline mode
4. Then go to administer and change theme to Garland
5. Turn off all non core modules
6. Now delete out all folders and files from public_html (within its Drupal folder) except
1. Sites (IMPORTANT)
2. Files
3. Any other non standard files or folders
7. Copy up Drupal new version folder except sites folder
8. Upgrade site
1. In browser open www.websitename.com/update.php (available from site building - modules page)
2. Run the upgrade script
3. Go back to administer page and turn on all non-core modules with no prior dependencies
4. Check site
5. In browser open www.websitename.com/update.php
6. Run the upgrade script
7. Turn on modules progressively - do required ones first, dependant ones second. Run upgrade script after each.
9. Change to original theme
10. Check site thoroughly
11. Review all module settings
12. Go to admin settings and site maintenance and put site into online mode
13. Pat yourself on the back :)

For any sites that have customised modules or other files – eg htaccess file, we replace these or edit as required also.

Here are the official Drupal version upgrade notes.