Well, to answer your questions, the second motherboard is definitely better, but only if you need really good graphics. As in REALLY good graphics, the kind only a 3D gamer needs. Basically, the difference is in the speed of the AGP, the slot where you put your videocard. Faster is better, but not always necessary. Asus is a great mobo manufacturer, you've made some great choices with them.
Sony makes some great CD-ROM products, hoiwever I would be more comfortable with something from Kenwood, Toshiba, or TDK. It's really personal preference.
I personally would go with an Nvidia video card, like a TNT2 or GeForce 2 MX, the cheap one. It's about $120. Your soundcard is perfect. The speaker choice depends on your preference, with a budget box, Labtec LCS-2514 would be the best choice. They run about $50, you can get them at Fry's or similar places.
I think the most glaring thing about the site is the case choices. The power supply should be at least 300W. You could probably just buy an ATX case separately, some recommendations for your price range are Inwin, Enlight, and Fong Kai.
You seem to have found a very good site for buying your stuff, at very cost-effective prices. Congratulations on choosing a custom system, we're here to help if you have questions. Good luck!!!