OS3.9 is really nice - but in my experience and usage, I do not like running it on anything less than an 040. It felt pretty slow on my 40mhz 030 equipped A1200 when I had it and I recently installed 3.9 on my 25mhz A3000 - to which I quickly un-installed it and went back to 3.1.
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Hmmmm - I mainly use OS 3.9 on my A4000PPC. On the 68060@50mHz the speed is quite acceptable, but this may be due to the fact that my harddrives are attached to the UW-SCSI host adapter.
Initially I had an HD attached to internal IDE and that way the system was not so responsive. So I switched to SCSI and disabled the IDE...
I also have an 40mhz 030 equipped A1200 with OS 3.9., but haven't used it for years. I can remember that it was of course slower than the A4k, but I would think dropping the IDE in favour of an SCSI host would most likely speed up the system equally.