Well one of the latest issues out there in the development would is this issue of infected websites that drop malware. Most of the time this is caused by not keeping your code up to date in the most secure methods of coding. Most open source code is taking this into consideration. However if its project is behind in updates or if you are using an old version of the script you can be faced with malware infections. Custom code is very at risk unless it is coded properly and is kept up to date.
I have developed a application that once installed on your server will scan all scripts and produce a list of infected scripts. It will should you the type of infection and what line number in the script that is resides.
Below is an image of a clean scan:
Below is an image of an infected scan:
If this is a service you would like please let me know at scottv@scovol.com.
I am currently working on developing an up to date malware site list that will be loaded into the scanner automatically.