Armory offline wallet is the best. Use it on a permanent offline PC and interact with a USB stick through it. Make sure the hard-disk is encrypted and also hide your passwords very well, its the best security that i can think of, secure enough to hold 1 billion $ woth of bitcoin in it.
But only if you know how to secure it propertly.
Otherwise for smaller sumps Xapo, Blockhain.info and other online wallets are pretty decent too.
I recommend a Qr Code over USB. See
https://github.com/hank/armorycompanion-python/Well i use an empty USB, unless the virus can put itself there without i detecting it its very unlikely.Also reformatting it after every use, just for safety.
Also you can use a different CD every time you use it and burn it the offline tranasaction file to it.
The QR Code looks nice , but then again the risk is that it can have a backdoor and put more info in that qr code than needed...
Not saying that it is going to happen but if the virus has the ability to copy it into the USB, install it in the offline computer/copy the important files, go back to the online computer and send it to the internet, you would be messed up. The QR code shouldn't have any backdoor since it is opensourced and you can check the qr code for anything. The hard disk idea wasn't very good since hard disk have limited lifespan and can be spoilt after some time.