Can you use Ninject 2.0 with VS2010 RC1?
I had similar issue... try targetting the full .NET 4 Framework, not the Client Profile.
From my understanding System.Web is in .NET 4, but not the .NET 4 Client Profile. So for your assemblies, in which you are taking advantage of full Ninject compiled against 3.5 sp1, you will need to ensure they are not targeting the .NET 4 Client Profile but the full .NET 4 profile in order for the dependency on System.Web to be satisfied.
Even if it is compiled for .NET 3.5, the assembly should be able to run in .NET 4. Here's a nice picture.
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