Good discussion here: https://askubuntu.com/questions/22215/why-have-both-mnt-and-media
The new standard is that /media is where the system mounts removable media, and /mnt is for you to mount things manually.
and
Another important difference not mentioned yet is that devices mounted under
/mnt
will not appear in Nautilus' left pane, whilst those mounted under/media
(as well as auto-detected devices that are not mounted yet) will.