Considering the two different approaches as you are (a good consideration in IHMO). Typically on-board is cheaper and awhile back it was poorer quality but the quality is improving (in particular sound). Separate cards cost more but allow you to plug the cards into your next board and typically that's it except for a few drivers particular to the new board. If you change hardware often I might argue for separate cards but if you're going to setup and that'll be it for a couple years then the cards become outdated and you'll have to get all new stuff next time anyway.
I went the separate card route about a year ago because the baord manufactors were changing HD controllers, for example RAID versus SATA. If you change brands of motherboards or they change HD controllers you will have to reinstall the OS (some folks do anyway as part of their practice). Again this is a problem only if you're changing hardware frequently.
There really is no correct answer, just what you rather do.
I bought the "s" version just because I like "bells and whistles". Eventually you'll want(have)to get a board with SATA, but for know it's not a big deal. I would get the cheaper board and wait to get an all options board when PCIexpress comes out.
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