Modal Pop-Ups Not Supported
Solution -Create a User Control that expands the entire canvas and set the opacity to .05
as seen on ScottGu's sample Silverlight application
http://weblogs.asp.net/scottgu/pages/silverlight-2-end-to-end-tutorial-building-a-digg-search-client.aspx
Datasets not supported
Solution - Use LINQ to XML that can read XML into a generic list for databinding purposes
Master Pages not supported
Solution - Create a parent XAML page, and have the rest of the application created using User Controls so you can switch between them
Namespace problems occur when using the AJAX toolkit together with the ASP.NET Silverlight tag.
Solution - Use the OBJECT tag instead of the ASP.NET Silverlight Tag.