I would not build a DDR2 machine right now. If you follow the layout in the thread in my signature, we might be able give a lot better build for what you're planning on spending. Since you said you're planning on building, I assume you haven't actually bought parts yet, right?
If the OP wants an ION-based HTPC right now, DDR2 is the only choice. Otherwise, it's wait for the next rev of the Atom for DDR3. Even then, no idea how long it will be before the new Atom platform makes its way into ION mobos.
So, yeah, more info needed, like does it have to be ION?
I looked and looked when I put together my HTPC build but was unable to find a micro-ATX ION mobo. You're not going to find a mini-ITX case with room for more than one slot. If you want to go with ION you're going to be stuck w/o much room for upgrading later on -- maybe a single slot. You could fit a mini-ITX mobo in a micro-ATX case which would give you room later to ditch the mobo and get a mobo that would support a 2-slot card but do you really want to do that? What's great about mini-ITX is the whole small form factor thing. You might as well at that point go with a micro-ATX mobo. But, like I said, no micro-ATX ION. The next best thing is to find a micro-ATX mobo with GeForce 9400 IGP. I found one available: http://www.newegg.com/Product/Product.aspx?Item=N82E168.... You could pair this with this CPU: http://www.newegg.com/Product/Product.aspx?Item=N82E168... and now you've got something close to ION (same IGP and about the same $$$) but in micro-ATX form however more upgradeable down the road when you want to ditch the IGP and more powerful than Atom.
So, you've got to figure out what you really want -- a small HTPC that's not going to be upgradeable (mini-ITX) or a larger HTPC that will be upgradeable. Today, you won't get both -- at least I couldn't find it.
Just one thing I don't understand. If you're going to use the HDMI graphic output from the motherboard, why do you need a case that can handle a dual slot graphics card?
At any rate, this Antec HTPC case will suit your needs, if you don't mind using low profile graphic cards. This case accepts both m-ATX and ITX motherboards. A couple of other notes:
1) That the expansion slot on that motherboard is PCI (not PCI-E).
2) I saw no where in the description that the SATA slots are RAID capable. With only one expansion port, you're going to need to choose between a graphics card and a RAID controller card.
Probably your best bet (as Dougie suggests) is going m-ATX.