I just pulled my hair out looking for what caused this, but eventually found it after scanning the module files. The issue was that overriding hook_theme_blocks wasn't possible in some theme. The version in the theme wouldn't get called at all, even after rebuilding the theme registry by clearing the cache. The culprit was the Block Translation module.
Some modules do provide their own CSS files. Themers might not always like what's happening in there and want to provide their own styles. You can remove the file (using preprocessing) or you can just replace the file with your own in your theme.
An example? Take the link module, which adds a link field type to CCK. This module has provides a CSS file : link.css. Suppose you have uploaded your module at sites/all/modules/contribute/link, we now have a file sites/all/modules/contribute/link/link.css.
Today I was looking for a way to customise the confirmation e-mail sent by the webform module. It appears that it's possible to customise this mail per form. By looking a bit further I discovered a file I had overlooked all of the time. This little file is called THEMING.txt and it delivers what is promised: it shows you how to customise all things Webform.
What will you discover there?
Great! This teaches you how to customise the 3 parts in a webform subimission process: form display, confirmation screen and confirmation e-mail.
Go ahead and read it here: http://cvs.drupal.org/viewvc.py/drupal/contributions/modules/webform/THE...
I've just launched my new portfolio website.
Go visit it at davyvandenbremt.be.
I need to take a break now.
Some really interesting posts are coming up!

A 'snippet' is "a programming term for a small region of re-usable source code or text", says Wikipedia. Of course there are a lot of snippets available for such a popular environment as Drupal.
In the Drupal handbook, the official documentation for Drupal, you can find two sections with snippets. One is for general PHP, SQL, view, block, ... snippets. The other is for theme snippets.
There are also two unofficial resources available, DrupalBin, a pastebin website for Drupal, and Drupal Snippets. The second one has few snippets available right now though. So the most dynamic resource to keep an eye on is DrupalBin.
There's probably a few more. I invite you to submit those in the comments.