Is wine vulnerable to windows based viruses?

Answer is yes..
Windows applications work the same way in Wine as they do in Windows. So in short:
Yes - Security is an issue.

Long answer with infos:

http://ubuntuforums.org/showthread.php?t=543419

For security issues:

You probably should be behind a router with firewall or install something like firestarter.

Ubuntu comes with a firewall installed: IPTables. Firestarter is just a GUI front end for it.

Now the next common question that people ask is there a way to "stealth/hack" your ports via IPTables config files without installing Firestarter as a GUI?

answer is: When you install Ubuntu, iptables is there, but it allows all traffic by default.

I can bet you that on a default install when you run the command

sudo iptables -nL the result you get is

Chain INPUT (policy ACCEPT)
target prot opt source destination

Chain FORWARD (policy ACCEPT)
target prot opt source destination

Chain OUTPUT (policy ACCEPT)
target prot opt source destination

=all traffic allowed ;-)

When you start using p2p applications you become extremely visible and you get all kinds of unwanted connection attempts. If your PC is sat there online with an (possibly unsupported and untrusted) application listening on multiple (or even unknown random) ports you really should have some control over the traffic. So you can learn iptables or use a gui frontend, hence my suggestion to use Firestarter or similar. For a desktop user a nice gui interface fits the Ubuntu philosophy much better than expecting users to correctly set iptables rules by hand and it's very easy and quick to set up. If you don't have iptables configured one way or the other your security policy comes down to only using invulnerable applications (no, I can't think of any either) and unbreakably strong passwords. Good luck.

Hope it clears your doubts..:)

Bhavani Shankar.