When you search for packages, the server does get what target framework your project's targeting but we ignore it. Until recently, the server did not have access to this metadata, but we do capture it now so we should probably start using this. This way
when a user searches for AutoMapper, we would show the highest version that targets your project's framework instead of the latest version all the time.
In the meanwhile, a hackier workaround for the discoverability issue might be
a) Add an empty lib directory to your package that targets net35. We will now assume that this package targets 3.5.
b) Add a dependency to your package pointing to Automapper.net35. http://docs.nuget.org/docs/reference/nuspec-reference#Specifying_Dependencies_in_version_2.0_and_above
This way people installing the package in 4.0 or higher get the right binaries, and people using 3.5 would get the binaries from the 3.5 dependency.