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Version 3 of SQL Server CE will eliminate a lot of the problems that developers have neen dealing with, working with SQL Server 2.  One of my greatest shocks when I first userd SQL Server CE was that if I left SQLCE Query up and connected to my database, when I ran my applicaiton that accessed it, I got a sharing exception.  No more with SQL Server CE 3 (Net yet available, due for Yukon B2 timeframe).

Also, the new Workbench allows you to run SQL CE queries on your handheld from the desktop, and more important, can show the execution plan, and accept hints (implemented slightly differently than on Sql Server).

The bad news?  Still no stored procedures, so it is still likely the database layer will have to be seriously refactored for Pocket PC use.