The different functionality of db4o is implemented in multiple assemblys. You need to include only the assembly which are required for you're application. Here's an overview:
This assembly contains the core functionality of db4o. It doesn't have any dependencies to other assemblies
This assembly contains the LINQ-support for db4o. It has a dependency to Db4object.Db4o.dll and Mono.Reflection.dll.
In Visual Studio, you don't need to add the Mono.Reflection.dll as a reference, Visual Studio will include this dependency automatically.
On the .NET compact framework, this assembly depends on Cecil.FlowAnalysis.dll and Mono.Cecil.dll instead of Mono.Reflection.dll.
This assembly contains the client-server support for db4o. It depends on the Db4object.Db4o.dll and nothing else.
This assembly contains the ADO.NET Data Services implementation for db4o. It depends on the Db4object.Db4o.dll assembly. While this assembly doesn't depend on the Db4object.Db4o.Linq.dll, you still need that assembly for the ADO.NET Data Services LINQ query support.
This assembly contains some additional features and functionality for db4o, like monitoring capabilities and Java support.
This assembly contains some additional features and functionality for the db4o client server support. Like SSL and monitoring capabilities. It depends on the Db4objects.Db4o.dll, Db4objects.Db4o.CS.dll, Db4objects.Db4o.Optional.dll and the Db4objects.Db4o.LINQ.dll assembly.
This assembly contains the native query optimization. It depends on Db4object.Db4o.dll, Db4object.Db4o.Instrumentation.dll, Cecil.FlowAnalysis.dll and Mono.Cecil.dll.
In Visual Studio, you don't need to add Db4object.Db4o.Instrumentation.dll, Cecil.FlowAnalysis.dll and Mono.Cecil.dll as a reference. Visual Studio will include this dependency automatically.
Note that native queries work also without this assembly. However the queries cannot be optimized without this assembly and will run a lot slower.
This is a command line tool for doing various enhancement to your classes. It depends on Db4object.Db4o.dll, Db4object.Db4o.Linq.dll, Db4object.Db4o.Optional.dll, Db4object.Db4o.NativeQueries.dll, Db4object.Db4o.Instrumentation.dll, Cecil.FlowAnalysis.dll and Mono.Cecil.dll
This is the MSBuild fronted for built time enhancement. It has the same dependencies as Db4oTool.exe and Db4oTool.exe itself.