Since I am among other things, a member of the Drupal security team, I sometimes get contacted about the security of particular modules or sites.
Today was such a day. A Drupal site developer had some suspicions about a contrib module being unsafe, since three of his clients' sites got "hacked". I asked about the symptoms and was told that a call to an advertising site got inserted into index.php.
This fact alone told me two things:
1) It is not Drupal specific; index.php is used by many PHP applications.
2) It is unlikely that Drupal was the attack vector used. Most systems do not allow the Apache user to modify PHP files.
A cursory look at the named module also didn't reveal anything particular unsafe.
I shared these observations with the concerned developer and I also suggested that somebody guessing the passwords or using a trojan might be responsible.
Later he indeed confirmed that he found a trojan on his machine, and now had to change passwords and check sites for all of his clients (A longish list).
Hopefully he will clean up and secure his desktop too.
What can one learn from this? There's more to Web security than only Web servers and Web applications.
One shouldn't feel too bad if things like this happen, however. After all, just a little bit later it was discovered that this very website (association.drupal.org) was about to be converted to a link farm due to an inexplicable error in site setup.