How to protect against wallet theft?
Physical access: 

Minimise your risk by using a deterministic wallet with Armory, and enabling extreme encryption and key stretching. The program will let you configure your wallets settings, and you can make it sting to the point of being completely ridiculous, seconds to open is enough to stop any attack on the password. 

Malware 

There is no protection against malware on a computer with a wallet. These exist already as pre-made tools, so it's hardly a stretch to think you might be infected. 

Use a hardware wallet like the Bitcoin Trezor or a split-wallet with an offline portion with Armory. 

In a split-wallet a computer is kept air-gapped and stores the private keys, and a separate one is used to manage the wallet. Transactions are ferried by USB drive between the machines, so the offline wallet is never at risk of compromise. This is the best option for storing large amounts of funds safely.