What you've got isn't bad so far, I would personally look for a more HTPC orientated case such as these:
Antec fusion (which is a very nice case, nice VFD display in the front, plenty of front ports and vol control, also very cheap compared to most)
Silverstone LC16M (EXTREMELY nice, but this is where things start to get a wee bit expensive)
(This is obviously optional. I'm a bit obsessive when it comes to that, if it doesn't look like it belongs near my hifi stuff, it gets hidden behind things :P) and also noise could be an issue with a HTPC so I suggest going to as much passively cooled stuff and quiet fans as you can.
With the sound you can go either way, you can either run the sound through your AV receiver/amp which if you have a decent set up will provide far greater sound or you can as you said get the 5.1 speakers, adding another load of speakers would probably create more clutter than using a separate box though.
Onboard sound is OK, I wouldn't use it for anything like this though, my personal preference is M-Audio, they have fantastic sound cards (the Revolution 5.1/7.1 are fairly cheap and are excellent cards)
Motherboard I look for eVGA normally as they provide a lifetime warranty and out of the 4 I've used in builds they've been rock solid so far.
Ram, if it's just a HTPC and light gaming 2gb will do fine, though if you're looking to play 1080p content and the like, 4gb would probably help you along.
Another thing to consider would be do you want to play HD-DVD's, if so you're going to need a HDCP compliant graphics card, there are a few around which really aren't that expensive, I believe the 7900GS does and the 8XXX series nvidia cards do and since you can pick up an Xbox 360 HD-DVD drive for next to nothing which you can use with the pc, why not? :P