Well, it depends.
When you bought an Amiga, it came with Kickstart ROMs and a set of disks, so obviously you have the right to use the full OS.
If you bought an upgrade pack for OS3.1, it came with ROMs and disks. So, thats the same.
Now, I believe you can actually buy Kickstart 3.1 roms on their own these days. I don't know if buying this gives you the right to a copy of the disks or not, but i doubt it. At least if you want to legally use OS3.5 or OS3.9, you need to own a 3.1 rom set *and* the CD, which are sold seperately.
Edit: Also, the Amiga Format cover CDs used to come with a licenced set of disks for Workbench 3.0, so if you buy some 3.0 ROMs and still have an AFCD somewhere, you have the full set for that.