How does this site infecting script work?

Notice the replace call after the giant messy string: .replace(/#|\$|@|\^|&|\(|\)|\!/ig, '').

It removes most of the special characters, turning it into a normal URL:

evil://dyndns-org.gamestop.com.mybestyouxi-cn.genuinehollywood.ru:8080/softonic.com/softonic.com/google.com/livejasmin.com/videosz.com/

(I manually changed http: to evil:)

Note that the regex could have been simplified to .replace(/[#$@^&()!]/ig, '')

If you look at the script, you'll see that it's a very simple script that injects a hidden IFRAME containing the path /index.php?ys from the same domain.

I requested that page in Fiddler, and it had no content.

These answers might help you understand the nature of the malicious JavaScript code but what you should be looking for is a way to close the loophole inherant in the Joomla engine. Pre-packaged frameworks are prone to loopholes, either intentional or unintentional, especially when you take into consideration that they are engineered to work on unix, mac and windows environments.

My work requires I run many domains, applications and frameworks on many types of servers and systems for clients and myself. Over time I've seen more and more bots crawling these systems looking for known loopholes/entrances by-way of back-door entrances created by those frameworks. Good thing when I use any type of framework, which I seldom do, I make sure to rename most if not the entire file structure to rid myself of those pesky loopholes/back-doors. At the very least you can rename directories which will throw off most bots, but my way is to completely eliminate references that give clues as to the nature of the framework, which includes renaming of the entire file structure not just directories. Always keep a map of the new naming conventions relative to the old naming conventions in order to make adding plug-ins to your base framework a snap. Once you get the hang of this you can go as far as programatically renaming the entire framework filestructure for quicker results, this is especially useful when having to deal with clients needing to be able to update their framework with plug-ins and the like.

It just does a regex replace on the script url to give you

NOTE: DO NOT FOLLOW THE BELOW LINK (inserted ** to deter the copy-pasters)

http**://dyndns-org.gamestop.com.mybestyouxi-cn.genuinehollywood.ru:8080/softonic.com/softonic.com/google.com/livejasmin.com/videosz.com/

as the src

It uses the replace function to replace the rubbish chars using regex, nothing wrong with the code:

 ........replace(/#|\$|@|\^|&|\(|\)|\!/ig, '')