I suggest Armory.
One "live" computer with armory, with "watching-only" wallets.
Another small computer completely offline, doesn't even need the blockchain. Has the same wallets, but including the privkeys.
Create a tx, move it to your offline computer via usb-key, it signs, you send the tx on your online computer.
This, with several independent wallets (like one small wallet which has the funds directly on the online computer too) is pretty secure.
Nah. Once a malware has root/admin rights on your computer, it's game over. Any software, anything in RAM can be read, written, manipulated, replaced, you name it. Heck, there are malware who run your whole windows in its own virtual machine!
You have, at least theoretically, a chance when using a TPM. Then it's "just" the question if there is no bug or backdoor in it.
Either way, Linux and common sense goes a long way!
I'm note sure I understand exactly how this works and I've never user Armory before but I'll do some testing with it.
There's a tutorial about offline wallets in Armory right here:https://bitcoinarmory.com/using-offline-wallets-in-armory/
For now, Armory+Offline is the most secure practical way to handle bitcoins, second only to paperwallets printed from a livecd. Which you can't securely redeem ;-)