One truly basic/fundamental measure you can take is use a HIDS, such as
AIDE. You should create the initial baseline right after a fresh install from trusted media and before connecting to any network. While this is a passive (and some might even say
old school) way of detecting unauthorized activity, it's still very effective. If you want to go for something more advanced, maybe look into solutions like
Samhain. Tools such as
Rootkit Hunter are a really good idea to have in your arsenal too. If you're running Ubuntu, it might be beneficial for you to become acquainted with the
AppArmor mandatory access control solution it includes, as that can prove to be an extremely useful defense mechanism from certain types of attacks. Using a virtual machine (such as
VirtualBox, for example) to keep high-risk activity isolated from the rest of your system is also something I would highly recommend as part of a risk-reduction endeavor. As for limiting the spread of Windows viruses,
ClamAV is a free virus scanner which is commonly used on GNU/Linux for that purpose.