For a quick overview ...
CLR Enhancements: Although the CLR uses the same model as 2.0, you can read here about the improvements/changes to the assemblies.
Compiler Enhancements: New VB.NET 9.0 compiler and support for changes to C# 3.0 like expression trees, lambda methods, extension methods, static reference for anonymous types etc.
LINQ: Probably the most revolutionary change in the 3.5 framework. LINQ to XML, LINQ to SQL, LINQ to Objects and LINQ to Datasets. Along with functional programming, LINQ is an outlook change to programming in C#.
Performance Improvements: Quite a few performance improvements have been made in 3.5. ADO.NET gets paging support as well as synchronization from caches at local and server datastores. Also performance improvements for multicore CPUs.
Networking changes: Peer-to-peer networking stack, including a managed PNRP resolver.
Windows Information APIs: New wrappers for WMI and Active Directory Services. WMI 2.0 gets a managed provider.
ASP.NET: New implementation of Client Application Services as well as 3 new ASP.NET controls. Also AJAX programming for ASP.NET is easier and better performing.
Windows Communication Foundation: WCF now works with POX and JSON data.
Windows Presentation Foundation: Newer plugin model for creating AddIns. SilverLight CLR is also part of the .Net Framework.
Misc: The C/C++ get a standard template libarary (STL) so that these languages can use share .NET libraries
for some extra reading ...