If you don't like noise, you could take a look at
silentpcreview.com | Everything about Silent / Quiet Computers
They also deal with smaller PC's, even mini-ITX.
And for the harddisks: 2.5" harddisks tend be be more quiet, although I might be tempted to suggest a flash disk these days. You could use the 3.5's in a NAS in another room.