Why waste money when you can have everything for free and 3.1 runs better? 3.9 isnt even up to date but you have to download boing backs and updates from Aminet if you wish to use latest versions.
OS 3.5/9 support hard drives >8GB (new scsi.device) and have ATAPI support for CD ROMs, for which AFAIK there's no free alternative on Aminet.
Varthall