During the initial installation, I did not activate full disk encryption since I just wanted to try out QubesOS a little. Turns out I enjoy it a lot. I used QubesOS for a while now, setting up many VMs, but my system is not encrypted. Is there any way to activate disk encryption now, to obtain basically the same result as I would have if I had activated it right from the start?
Using “Backup Qubes” on those Qubes you have changed from / added to the default, reinstalling QubesOS with FDE and then “Restore Qubes” should work.
Recommended: Test restoring on at least some of the backuped Qubes before reinstalling, just in case … 
(Maybe somebody more qualified knows a better way of doing this, since I am just getting started with this great OS myself … )
I think @Spheres has the right idea. There may be a way to do it without reinstalling but I think reinstalling Qubes OS with full disk encryption is the most straightforward approach. Then restore your VM backups.