FYI and discussion purposes... Do you have lots of JavaScript coding in the header section of your web pages? Do you re-list your CSS styles at the top of every page? Do you have JavaScript coding spread throughout your web pages? If you answered yes to any of these questions your site may be driving away search engine spiders and losing search engine position ranking. http://tinyurl.com/8dz8t
Search engines generally scan your website looking for text (e.g. content). If the upper portion of your website is mostly CSS tags and JavaScript, then you are limited and/or diluting the portion of your "intended content" with the "non-intended content" (e.g. CSS tags and script). If search engines only scan the first xxx of a page, you may have completely (or at least partially) prevented them from finding your desired keyword phrases and, in essence, blocked them. IMHO. BTW, you may want to read the article linked from the original message which explains this in greater detail.
I remember this issue being prominent back in the day, when Google was only capable of reading a limited number of characters. I'd place a couple bucks down to suggest that this has been fixed, and that none of the other engines have this same limitations, but exporting your JS and CSS would still be considered best practice, no?
Having css and javascript in the html won't hurt rankings at all. Why would it do that? The parser will simply use that info to guess the relative size of the text that follows. I have never seen a person go to a web-page, then check its source and says: "wow, lots of javascript and css. this page is of low quality. I am not going to read it." This is just presentation. What matters is the info and the support it gets from links.