sjrsaj: First congrats on getting your 4000 going again! As for 3.9, I can say that it makes using hard drives bigger than 4GB easier.... you do know about the dreaded 4GB barrier, right? Without patches, once you have data on the HDD that crosses the ~4GB barrier... poof goes that data... a bit over-simplified, maybe. Others here can be more specific....
I personally have bought 3.9, and even 3.5

But mainly to support Amiga development .... sigh....
IMO, it's not an earth-shattering upgrade aside from the big HD support....