A client of mine recently accidentally unpacked a drupal folder (specifically, drupal 6) into the modules directory. What this means, unfortunately is that the next time drupal is asked to render the page, it looks in the modules directory, sees the new drupal folder, and thinks that the modules folder inside THAT drupal installation is the place it should look for modules. So you'll get a slew of errors, more depending on how many modules it took to render that page.
This one took me a couple tries. If you're installing Drupal into a folder on an account (this particular case was with GoDaddy) in order for clean URLs to work and everything, you have to modify the .htaccess file. The part where it has:
# If your site is running in a VirtualDocumentRoot at http://example.com/, # uncomment the following line: # RewriteBase /
This was with CCK 6.x-2.2 (shouldn't matter, all this functionality's been in CCK since back in 4.x I believe) and I needed to make a CCK value for a content type that had dynamic options to select. Basically I'm trying to mimic some of the functionality stories supply with child and parent nodes, except with regular content types. So I added a field to my custom content type.
Looks like I need to do something crazy with the allowed values list then. So I look down the list and see this disclaimer for it:
Typically I migrate sites by copying the directory to its new location, creating a blank database, resetting the settings.php file, then enabling the Backup/Migrate module and importing the old database. All my modules, settings, everything is usually correct.
This is one of the points for a website that I think will tell you quickly whether you're talking to a designer or a web developer. I recently came up with a design for a website that needed a "rough, emo grunge" look that's pretty popular these days. Well what's a grunge site without a rough font or twenty? I tossed some in there, and said I'd worry about it later.