Here is a small unexpected aspect of the NetLogo-Mathematica Link. There's also an easy workaround, but it's surprising that when starting the link with …
<<NetLogo`NLStart["/Applications/NetLogo 6.0.4"]
and (eventually) finishing with
NLQuit[]
but keeping the current Mathematica kernel running, and starting up the link again with an intended different version of NetLogo, like this
<<NetLogo`
NLStart["/Applications/NetLogo 6.0.1"]
the actual NetLogo version usage doesn't change. The 6.0.4 version still boots. The workaround is to quit the Mathematica kernel before using <<NetLogo` again.