No modern OS is 100% free of viruses or hacking - and, even if it was, people can always just steal your computer. Assuming you can't be safe nobody will access your machine, is it still safe to keep your accounts in your PC, as long as they are encrypted with a strong enough passphrase? Or will that passphrase be useless in the case somebody gains full access to the backup files?
In general, if you carefully generate your keys offline and on an untampered live system, with a strong passphrase, you are good to go.
In opposition to any other anwsers recommending cold/offline storage, I suggest strongly not to use offline storage. There are so many popular examples out there where huge amounts of value disappeared from cold storages that the common way to store high value is using multisignature wallets.
Ethereum makes it pretty easy to generate multisignature contract wallets. Use them. They are the safest option, as long as all underlying accounts were carefully generated offline, on live systems and the keys are well encrypted.
They would have to crack your password to be able to steal your ETH, so it would be as secure as your password is strong. But if a keylogger virus was on the computer logging all your keystrokes, then they could see what your password is.
I recommend putting any large amounts of ETH in accounts into cold storage: save the account file inside an encrypted / password-protected RAR file (using WinRAR on a unix / linux variant) with a different password on the RAR file, then delete the installed account file after a full backup to USB Drive / CD / etc...then you are much safer.
EDIT: I agree with 5chdn that multisig is even more secure, in fact I use that myself with cold storage on the multisig-related accounts. I was just trying to keep my response focused on account security.