Linux – standard place in the Linux file system to put Windows shared folders

For more data on the layout of Linux file-systems, look at the Filesystem Hierarchy Standard (now at version 2.3, with the beta 3.0 version deployed on most recent distros). It does explain some of where the names came from:

• /bin - Binaries.
• /boot - Files required for booting.
• /dev - Device files.
• /etc - Et cetera. The name is inherited from the earliest Unixes, which is when it became the spot to put config-files.
• /home - Where home directories are kept.
• /lib - Where code libraries are kept.
• /media - A more modern directory, but where removable media gets mounted.
• /mnt - Where temporary file-systems are mounted.
• /opt - Where optional add-on software is installed. This is discrete from /usr/local/ for reasons I'll get to later.
• /run - Where runtime variable data is kept.
• /sbin - Where super-binaries are stored. These usually only work with root.
• /srv - Stands for "serve". This directory is intended for static files that are served out. /srv/http would be for static websites, /srv/ftp for an FTP server.
• /tmp - Where temporary files may be stored.
• /usr - Another directory inherited from the Unixes of old, it stands for "UNIX System Resources". It does not stand for "user" (see the Debian Wiki). This directory should be sharable between hosts, and can be NFS mounted to multiple hosts safely. It can be mounted read-only safely.
• /var - Another directory inherited from the Unixes of old, it stands for "variable". This is where system data that varies may be stored. Such things as spool and cache directories may be located here. If a program needs to write to the local file-system and isn't serving that data to someone directly, it'll go here.

/opt vs /usr/local

The rule of thumb I've seen is best described as:

Use /usr/local for things that would normally go into /usr, or are overriding things that are already in /usr. Use /opt for things that install all in one directory, or are otherwise special.

I'd almost certainly suggest using /usr/local.

Globally accessible user scripts can be placed in /usr/local/bin. Small amounts of associated data could also go into bin. Or you may wish to separate out the data into /usr/local/var or /usr/local/share.

By doing this you'll be quite sure that anyone FHS familar will be able to locate them pretty quickly without any prior knowledge of the particular system.