Personally, I would like the JREF Wiki to link to, and be linked from, the JREF Encyclopedia.
Two reasons:
1. The JREF Encyclopedia is not being continuously updated, as the Wiki is. It's more like a fossil of Randi's writing than a living resource, but it does have good arguments in it.
2. I think that both resources are useful, BUT its difficult to link directly to articles in the Encyclopedia. So the Wiki is a much more useful resource when discussing new issues.
By the way, if there ever was to be a merger between the SkepDic and the JREFwiki then I'm all for it.