I have the following convention for most of my projects:
/src /Solution.sln /SolutionFolder /Project1 /Project2 /etc../lib /Moq moq.dll license.txt /Yui-Compressor yui.compressor.dll/tools /ILMerge ilmerge.exe
You'll notice that I do not keep external libraries inside the source folder. I'm also very interested in using NuGet but don't want these external libraries inside the source folder. Does NuGet have a setting to change the directory that all packages are loaded into?