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I know that SharePoint 2010 uses .net 3.5 and since .net 2 (3.5 with sp1) has different CLR than .net 4, what is the best practice to use Entity Framework 4 (4.2) with it?
Is the web service (WCF service) the only solution for it?
If not, what is the best ORM similar to EF from simplicity and productivity prospective is recommended to use to connect to MS SQL Server? (may support oracle later)?
Yes. You have to do cross process call because your main process is .NET 3.5 and you need another process running .NET 4.0.
Other alternatives are for example NHibernate or LLBGen Pro. Both are supported in .NET 3.5. You can also try Linq-To-Sql or SubSonic.