If you are using IIS (5 or 6) prior to WAS, Windows services may be your best (only?) Good bet for hosting WCF services that communicate over named pipes or netTCP (anything other than HTTP).
In the third release of WCF Services programming (link), Lowy suggests using the Windows Server AppFabric in some situations and offers several options for self-hosting - when you need to use the service bus, and IIS 7.5 is not available for example. Pages 22 and 23 show some simple diagrams to help you determine when to use your own hosting through IIS, WAS, or AppFabric. I think the first chapter (maybe more) is available for free if you get a Kindle sample.
Apart from these scenarios, I'm not sure why you ever wanted to choose any independent hosting through WAS. I am curious to know if anyone has a good reason.
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