2006 MacPro - Worth upgrading for use as a VM host?

Short answer, yes.

The MacPro 1,1 can run 10.7.5 as it's latest OS. I have a 2008 Black MacBook which runs the same. Despite being on an OS from 2011, you can still run the latest version (v7.1.0) of VMWare Fusion. You can also jam 32 GB of RAM in there. Plus, the Xeon from 2006 will almost be comparable to a Core i5 from a couple of years ago.

Like you, I also updated to an SSD. Even though the RAM in my MacBook is only 2 GB, it is an amazingly fast machine considering it's specs. SSDs are simply amazing, they are the best upgrades you can make.

I also have a 2012 Mac Mini. I installed the maximum 16GB of RAM and a 240 GB SSD. I am able to run OS X as well as a Windows VM and 2 Linux VMs with almost no degrdation in performance.

It's worth noting 10.7.5 might soon be cut off from receiving security updates, however I imagine you can configure some networking where the VMs have internet access yet the host machine only has access to the local LAN.

I'd say go for it. That machine is far from dead, there are still some amazing things you can do with it.

The main limitation is that it won't run a more recent OS X version than 10.7 (Lion), which probably won't be supported with security updates for much longer. I wouldn't put it on the Internet, but it should be fine as a VM host on your LAN.

Definitely Yes

My 08 is still well worth keeping going - it's still my main machine, with up-rated GPU, SSD, & RAM.
I see no reason why it shouldn't be worth keeping an 06 going for a while longer. Maybe Bootcamp rather than VM, if you need what speed remains in the machine. As you have plenty of drive bays, I'd Bootcamp to a different physical drive, seems to save issues in the long run.

You can hammer Mavericks onto it too, if needs be - see Modernizing the 2006 and 2007 Mac Pro to Go Beyond OS X Lion [far too much to précis here, but it doesn't look very difficult, just fiddly]