I've not added external storage for the Mac Mini as when it comes back from where I'm working now, it'll talk to additional NAS. I put my 1Tb NAS in the loft, but the only place where the guys could place it safely was above my bedroom and I can hear it at night. I thought about enclosing it and piping air out of there but it's just too much hassle. So scratch that idea and it looks as though the NAS will be going back to my datacentre and I'll be upgrading the low-noise server I thought I'd retired to a silent one.
For the other audio related PC's, I've resorted to 2.5" drives throughout. The biggest problem with 3.5" HDD's is vibration, and many have a screeching noise that they exhibit while spinniing. It's not noticeable in a normal PC, but when you drastically cut PC/PSU noise HDD noise rapidly becomes the #1 problem. With external hard disks, vibration causes any surface on which the drive enclosure is resting to become a sounding board. Damping is a must. The thing is that all of the popular damping solutions for 3.5" drives on the market are designed to fit into 5.25" drive bays.
I wonder if the 3.5" drive mount on the port replicator is damped? You know, I doubt it somehow.
I've not seen much in the way of reasonably priced external enclosures which prevent vibration from passing through the case. My relatively low-cost solution for vibration at least is Foculpods (or any high-performance Sorbothane component) as far as the external backup HDD's for my utility PC's are concerned. In any case though, all the 3.5" drives I have are IMO too noisy for me to use in a "living room audio PC" context.
For the silent server upgrade, I'll probably be striping 4 or 5 100Gb 2.5" drives, each mounted with a Nexus Disktwin (or failing that, the Smart Drive enclosure) with a Belkin 2.5">3.5" converter.
As far as a Mac Mini is concerned, for near silent 160~200Gb class storage what you may have to do is to pick from one of these and add two 2.5" drives with converters:
http://www.cooldrives.com/firen.html
Maybe specifically this one:
http://www.cooldrives.com/dual-drive...ini-1394b.html
(Although that fan may need replacement/removal... with 2.5" drives, it could probably be removed)