Is there any utility that can be integrated into Files so that I can just right click a folder -> encrypt/decrypt? If not, would you recommend me any GUI software to encrypt entire folders? I've been trying cryptkeeper but everytime I try to create a new encrypted folder, it crashes.
Use Gnome Encfs Manager. It's not an official elementary app, and it doesn't work from within Files, but it's worked really well for me. You can have the program launch at startup, or you can just summon it from slingshot whenever you need it. The interface displays a list of your encrypted stashes, so you don't have to hunt them down. I like that I can have folders on my computer that are protected by a password so I don't have to worry if someone borrows my computer.
Be sure to use a strong password for the stashes, if you want to keep them secure. Also, although Encfs is a really good and convenient way to quickly encrypt certain files or folders, be aware that it isn't without flaws.
Install seahorse and seahorse-contracts.
sudo add-apt-repository ppa:elementary-os/daily sudo apt-get install seahorse seahorse-contracts
I recommend you remove the daily repo after installation to avoid getting updates that may break your system.
sudo add-apt-repository --remove ppa:elementary-os/daily