As for the A4000 and A5000, another quiet option for hard drive is a 2.5 inch laptop drive spinning at 5400rpm. These tend to be a lot quieter than big desktop drives. I put an 80gb 2.5 inch in the A5000 and it's practically silent (sans fan too). Yes I know I'm wasting 70gb of that drive but at the time I couldn't source a smaller one!
Also, the partition size possible on the A series. They are all limited to 1GB partitions, including the A3000, not 512mb. Perhaps people are confusing them with the Akai samplers which had a limit of 650mb partitions if I remember correctly.
My (now unused) A3000 still has a set of Jaz 1GB external disk cartridges and I can assure you they are full to approximately 900-950mb on each disk. The limitation that does exist however is that nomatter how large your hard drive you can't get more than 8gb out of it, and that will be 8x1GB partitions as best. Still plenty space for most people!
Putting any kind of high speed disk into these samplers probably isn't worth it as the limiting factor is the eide/scsi interface on the samplers motherboard itself. They are crushingly slow, although the A4000 and A5000 are quite a bit quicker than the A3000 when you use eide drives (yes, the eide is faster on the A4/A5 than scsi is.....go figure)
I use both on the A5000, the internal 2.5 inch drive for silent work, and periodically a backup to a 9gb external scsi drive to keep that disk in sync. I have considered the compact flash option from time to time, mainly because it would allow me to take a 3rd clone of my backup scsi disk back onto another cflash card.
The knobs can be replaced. I paid I think £40 for a set of 6 encoder knobs from a swedish electronics site (kept 1 spare in case one got killed in soldering) and these were soldered in as replacements for the failing originals. The A5000 has worked perfectly since.
I do agree with the comments that the yamaha samplers sound absolutely beautiful with really excellent creative effects. Yamaha were probably on the cusp of making the sampler to end all samplers, just as Akai probably were when they made Z8, just at the point that computers took over and destroyed the hardware sampler market. It's such a shame, because despite all the speed and capacity, software samplers aren't better for making music, they're just better for adding another thing you can do while sitting at your computer getting varicose veins, along with email, sequencing, surfing youtube, twitter, photoshop etc. Jack of all, master of none!