General use, when you can install software through your system's package manager then that's the preferred way to get software on your system. For the most part, those applications live under /usr

If for some reason you prefer to install the package manually, best practice is to install it outside /usr to avoid potential conflicts with existing system libraries. The /opt ("optional") system is a common place to install these apps. Many modern install scripts already default to using /opt

It's also convenient for backing up those apps.