From the info I’ve gathered, it seems that LUKS over LVM is the “proper” way as ideally you’d only want to encrypt swap, /tmp and /var. (/tmp and /var are places for temporary files, ie. opening a .zip archive. Swap is just RAM on your hard drive, so a place where your passwords could be stored) Encrypting the root (equivalent of “program files” in Windows) won’t make your system more secure, just slower. (If you live in a place where you need to keep the list of your installed apps private, you’d probably be fricced by using encryption anyways.) Home directory should obviously be encrypted ~~but for the best performance you should use file level encryption instead of block level. ~~ edit: Do your own research on the performance, a reply claims otherwise, though leaving root partition unencrypted obviously increases R/W speed.
The thing is that setting it up this way is pretty hard so distros generally use 2 easier methods to setup encryption. Either encrypt the whole disk (LVM over LUKS) or encrypt only the home directory. I wonder whether the latter is secure enough though. Mint for example does not explicitly state that swap, /var and /tmp are encrypted when you select “encrypt home directory” but on Cinnamon there is not hibernation option so there is a chance that Swap is encrypted, just with a one-time password, which gets generated on boot and deleted after shutdown. <— citation needed…edit: I’ve just tried hibernating in Mint without FDE and it didn’t work, you just get a new session after resuming, so that’s good.