To be honest os 3.5 and 3.9 are really nothing more than a copy of os 3.1 somebody at H&P customised. They look nice, and have some nice software, but they offer nothing new if you already have a good 3.1 setup.
3.1 + MUI + Classact (reaction) + any TCP/IP stack for networking (I use the one from the 3.9 cd) = Runs more software than 3.9 does, out of the box. If its a modern program you'll probably end up copying lots of libs from aminet, no matter which os version you use.