You're VS Team System project WSS sites run on ASP.Net 2.0, and SharePoint Portal server doesn't support 2.0 I don't think, even with the latest service pack. If you were just using WSS, it might be feasible (although I don't know about worthwhile) to combine them all. That's the major issue that comes to mind,although there are probably others. We faced a similar recently, we've basically decided not to implement Portal server at all right now and just use WSS with the added benefit of .Net 2.0 support. We also use Corasworks components extensively to organize and tie our WSS sites together. Anyone else have any insight they could share?