I had a similar issue. The answer of Achim put me on the right track, and for other readers:
Create a file, like example.nunit
, like this:
<NUnitProject>
<Settings activeconfig="local"/>
<Config name="local" configfile="App.config">
<assembly path="bin\Debug\example.dll"/>
</Config>
<Config name="dev" configfile="App.Dev.config">
<assembly path="bin\Debug\\example.dll"/>
</Config>
<Config name="test" configfile="App.Test.config">
<assembly path="bin\Debug\\example.dll"/>
</Config>
</NUnitProject>
All the file / paths (of the configuration and assembly files) are relative to the location of the NUnit file. Also the App.config, App.Dev.config, etc. file are just .NET configuration files.
Next when you want to run it for a certain configuration you execute it like this:
nunit3-console.exe example.nunit /config:test
More information about the format of the NUnit file is in NUnit Project XML Format.
More information about command-line arguments is in
http://www.nunit.org/index.php?p=consoleCommandLine&r=2.2.5