Lots of page not found in logs

Some time ago, I had lots of such messages, and it was an issue with URL-format somewhere (a picture in my custom theme, but that's not relevant here).

You can have two styles of URL's:
--- Absolute: http://domain.com/something/something_else, or just /something/something_else
--- Relative: something/something_else

The absolute ones are based on your document root, while relative ones are - well, relative, to the current document. You should always avoid relative URL's, as there are problems with URL-variables.

In my case, no clean URL's used, the current document was /drupal/?q=something and the relative path seen in my theme was images/foo.gif. Any smart browser builds the real URL like /drupal/images/foo.gif, which is correct, but there are also stupid ones (perhaps crawlers, yes) sending requests to /drupal/?q=something/images/foo.gif. See what happens? The relative path appended to the whole string, including the variable, so it's Drupal who gets the images/foo.gif part to deal with, not the webserver. In my case, the resulting "not found" page contained the image again, making it even worse: The crawler appended another occurence of the string, then one more... I ended up with thousands messages in watchdog, each repeating the string almost endlessly.

Okay, it was just a stupid crawler, not stripping the variables from URL. But you seem to be using clean URLs, and in THIS case the browser may not know what's a variable and what's just subdirectory. The problem with relative paths is then unavoidable... So make sure that all your URL's start with at least a slash (or better full "http://"). In a theme, you can just print base_path() in front of your path, to make it absolute.