I'm using Electrum & mew. Private keys are saved in password protected .xlsx lists and stored in multiple hard drives.
But still how can you protect yourself if a hacker has a RAT on your computer and can just copy your password whenever you type it in?
It doesn't matter, if your machine is infected a hacker might as well copy the wallet file, the mnemonic seed, password or whatever he/she wants. When a hacker has access, all bets are off.
I think one minimizes the risk is to install antivirus in your computer and then add certain authentication to your wallet. like sms verify so when the hacker has got the password you type. they will not be able to enter your wallet because they have to enter sms verify first to be able to access the account..