<p>I am currently developing a .NET application, which consists of 20 projects. Some of those projects are compiled using .NET 3.5, some others are still .NET 2.0 projects (so far no problem).</p>
<p>The problem is that if I include an external component I always get the following warning:</p>
<blockquote>
<p>Found conflicts between different versions of the same dependent assembly.</p>
</blockquote>
<p>What exactly does this warning mean and is there maybe a possibility to exclude this warning (like using #pragma disable in the source code files)?</p>

Basically this happens when the assemblies you're referencing have "Copy Local" set to "True", meaning that a copy of the DLL is placed in the bin folder along with your exe.
Since Visual Studio will copy all of the dependencies of a referenced assembly as well, it's possible to end up with two different builds of the same assembly being referred to. This is more likely to happen if your projects are in separate solutions, and can therefore be compiled separately.
The way I've gotten around it is to set Copy Local to False for references in assembly projects. Only do it for executables/web applications where you need the assembly for the finished product to run.
Hope that makes sense!