You sir, get -9,001 Internets.
There are huge repercussions for any website that gets blacklisted with the Stop Badware clearinghouse, the least of which is the inability to figure out exactly where the problem actually is because the company you work for's information for a webmaster to resolve the problem is ridiculously minimal. There are no notifications (unless you are signed up for Google Webmaster Tools) and restoring a website to normal globally can take anywhere from 48 hours to two weeks. There are millions of developers who rely on the PHP website daily for performing their day jobs and you've now made it that much harder for us to do our jobs.
Stop Badware needs a serious overhaul. At the very least, they should contact the contacts in the WHOIS record for the domain BEFORE doing anything. Give the website owners 24 hours to resolve the issue before blacklisting the site. And give them a heck of a lot more information to go on than some vague text.
Also, there are several anti-virus vendors out there who use the clearinghouse database for their products...6 to 12 months after the original blacklisting. So this will happen all over again 6 to 12 months from now. Finding contacts for anti-virus vendors for removing domain blocks is a lot harder than removal from the blacklist on the Stop Badware site.
The CORRECT solution for this situation was to find a contact at PHP who could resolve the issue quickly and amicably. Seriously, how hard is it to locate Rasmus' e-mail address? Always try to find a human contact before using Stop Badware. You can chalk using Stop Badware for the PHP website as being the dumbest decision you've made this year. Hopefully this decision of yours will raise the ire of the Internet just enough to force the company you work for to revamp Stop Badware so it doesn't suck, Google Webmaster Tools so they don't suck, and the reporting tools for sending information to Stop Badware so they also don't suck.