In all likelihood it wasn't a virus or malware - it's a bit too early for that and if it was we'd see way more stolen wallets. From what you've written, I'd say it's a targeted attack.
Depending on amount stolen, you may want to hire IT forensics expert. If it was a script kiddie you have a good chance of catching him. If you consider to pursue this, I suggest you turn your computer off ASAP.
Unfortunately, we gonna be seeing this more often as value of Bitcoin increases
The problem is that I can't shut the machine as this is my work machine. I doubt any forensic expert can do shit. Bitcoins are 100% non reversible and even if this "expert" were to find out the IP address of the person who got it there is no guarantee that it was his real IP and well I'd be spending more than 25,000 BTC just to chase this.
What I'm going to do though is shut the machine down and let the symantec antivirus clean the supposed infection it detected when I ran a scan of f-secure online scan (for some reason it detected a bunch of virus in the temp dir where the online scanner stores its temporary work - could be false). And then I'm going to backup my important data. Format and reinstall the machine.
Then I'm going to sell whatever bitcoins I have remaining, take it as a life lesson, and count this as a not so fun experimentation with cryptographic currency.
I am then going to focus on making plain old paper dollars and store them in a bank where at least I'll have the full force of society or some central government insurance backing me up - not to mention some recourse to the law in case of any theft.
Sorry for your loss.
On a lighter note, I thought you had gone crazy for a moment and had written "I am then going to focus on making plain old paper dolls and..." =P