Back up your files reinstall OS from a boot-up CD. Thats the only real way of making sure.
I thought we had to take off and nuke the whole site from orbit. Its the only way to be sure.
Considering how valuable are these digital goods, there would be no problem in investing time and money in developing some very nasty 0 ring rootkits.
Even if you scan with an AV a harddrive as slave or from a bootable disk, it still doesn't ensure the cleanness of a drive if it wasn't on a sterile environment... ESPECIALLY if it is running Windows.
Considering the AmiBIOS source leak, accessing ring 0 would be trivial, and a BIOS Rootkit would be impossible to be cleaned up by an AV.
I would normally not worry that much, but with bitcoins a certain level of paranoia is expected.
There is no need of worrying as long as you follow very simple rules:
Ideal:
1) Nuke everything and start from zero.
2) Make a new partition and install Linux
3) Never use root
4) Use that partition only for Bitcoins and never use it for leisure browse anything.
If you are using Windows 7 (if you are still using previous version, you better kill yourself):
1) Nuke everything and start from zero.
2) Create a user with user privileges.
3) Use sandboxie for browsing, even with Chrome. Thinking of it... better sandbox everything. Sandboxie is your internet condom. Cherish it, learn to love it.
4) Use Kaspersky Antivirus. Better something than nothing.