Aside from not using shared hosting at all, at least don't use shared hosting provided by a domain registrar. The combination of supporting millions of customers and hosting not being their primary business means hosting MUST be treated as a commodity for them to offer it at all. They're not going to have the people bandwidth to help customers clean up their sites after they're hijacked.
Stay away from Godaddy hosting at all costs.
The blog doesn't give any numbers, but it seems that a few of their shared servers were compromised, so a few thousand of sites at least.
One of my clients still host in there and her files were all modified around 1pm today.
What I find unusual is the kind of code added to all PHP files:
" $_8b7b="\x63\x72\x65\x61\x74\x65\x5f\x66\x75\x6e\x63\x74\x69\x6f.. \x6e";$_8b7b1f="\x62\x61\x73\x65\x36\x34\x5f\x64\x65\x63\x6f\x64\x65";.. $_8b7b1f56=$_8b7b("",$_8b7b1f("aWYoZnVuY.. "
If you decode that, it is an encoded "eval(base64_decode" to load the malware as hidden as possible.