I was always dead against onboard graphics, but my nVidia ion 330 atom board has completely changed my opinion, I think it's fantastic. 2 gigs of ram, 512 MB dedicated to GPU, job's a good 'un.
If you're talking about HD over freeview, forget about it, I have it on good authority that there are no tuners on the market for us in the UK that support HD over freeview. However, freesat is possible for free-to-air HD stuff, and other SD channels that aren't on freeview. I'm looking into this myself as I have an old sky dish on my house from the previous occupants.
Your ubuntu box will be seperate. LMCE can scan media on your hard drive I believe. Personally, I like to use the core as backup for my "normal" desktop PC, so all the media is there regardless of whether my desktop is switched on. I have an rsync script on my desktop to "sync" the two.
I swapped the fan on my ion atom board for a scythe mini, and it is now barely audible. Worth doing I reckon. Bear in mind this is my MD, not my core. My MDs are in the living area, so I go to great lengths to keep them quiet, especially the one in the bedroom. The core is in a cupboard, so I just chuck any old crappy fans in that (but not too crappy - the core is on 24/7 remember!)
Hard disks - if in doubt, go bigger, they are so cheap these days. I have 1TB just for media, which is all mine and my girlfriend's music, movies, series, backup, and my TV recordings, and it's plenty for us. But your needs may differ. I have an 80 GB for the OS.
Gyro mice/remotes - I always had a gyro air mouse, for the last 2 year or so, and I finally stopped using it the other day, it was just getting on my tits. Now I have a Nokia N800, and I think it is superb, very swish. Got mine on ebay for about 50 quid, which was actually less than the gyro mouse was 2 years ago. That said, if you have your heart set on a gyro mouse, I have one for sale