To the best of my knowledge there is little difference between 3.0 and 3.1; but there is a huge difference between 3.9 (plus Boing Bags 2 / 4) and OS 3.1; A good reason for KS 3.0 is faster booting. OS 3.9 adds a lot of support for non-gaming stuff. If all you use Amy for is games, then don't bother with OS 3.5/3.9, nor the excellent 4.1 (PPC required); but if your Amy has a B/CSPPC you should get OS 4.1, a very modern yet still very Amiga operating system. Also in my opinion, if you have an 040 or 060, then you should be running OS 3.9.
I wish the copyright owners of still useful software would get off their anal orifice and let it either go public domain, or let someone sell it again. It is absurd for us to have to "steal" software when we are willing to pay for it!