With virtualization, does it still make sense to use multiple mount points?
Solution 1:
Sure it's still useful. You don't want a runaway process to fill a log and cause / to go full disk. Also, if you're using something like LVM you can do online expansion of volumes.
With many VMs, you're going to want to separate IO anyway. You're going to probably want your databases on separate spindles and the only way to accomplish that is to have a separate mount point for your database's location. Databases aside, it makes for more granular flexibility down the road if you outgrow your original design.
So, in short, yes there are still good reasons for doing this in 2013.
Solution 2:
Nowadays, I would not use too many separate mounts, but probably a few key ones would be helpful in system administration.
Just 2 or 3, esp. with one that varies in size. This depends on what you are using. I would say just / (relatively stable) and /var (changing). Depending on the os and disk geometry, /boot may also be needed. /tmp is likely a tmpfs mount set up by the installer.
The changing (/var mostly, but could be just /var/log and /var/lib/mysql etc.) volumes are usually what you need to worry about and plan for expansion. So if possible, use lvm etc. to make resizing easier.