No time to really help much, but this is what i recommend...
Samsung Ecogreen hard drives for storage, they run extremely quiet and cool and are only about $75-80 per 1tb. I have 4 of them and really like them.
Get a SSD for your OS drive, they are fast, silent and cool. I run OCZ 30gb drives in both my HTPC's for about 6 months and they have worked great
Will you game on this pc? If so get a dedicated video card, if not just get a 8100 based mobo with HDMI and a digital audio out
Get a keyboard with mouse/touchpad built in, you will thank me later. I use a Logitech Dinovo mini and a Logitech Mediaboard with mine