Hi Toby,
I'm not working on OSX so I'm not sure about the command line problems.
Usually you need the install path in your environment (i.e. PATH variable under windows) so the shell can find the executable.
Under Linux I would just set an alias to launch Nuke (i.e. alias nuke '/vol/appls/Nuke4.7/bin/nuke' - or wherever the files live on your system).
Apart from that, once installed shouldn't Nuke show up in your Applications folder so you can launch it via the finder?
As for gizmos and such:
If you're lazy you could just dump all your custom files into Nuke' plugins/user folder but that's ugly.
Nuke should automatically create a '.nuke' folder in your home directory and source anything that lives in there and also anything that lives in the folder(s) set by the NUKE_PATH environment variable should it be available. In those locations you can use an init.tcl file (which will be sourced for both UI interactive and render sessions) to add arbitrary plugin paths like this:
CODE
plugin_addpath
Use a menu.tcl file in your plugin path to create the UI for a tool. This file is only sourced for interactive sessions so make sure you don't put anything in there that may be needed in batch render mode.
Use the menu command to create a menu entry and call whatever gizmo/tcl-command you want:
CODE
menu "User/Gizmo to save the world" SaveWorld
This will create a new menu called "User" with an item called "Gizmo to save the world". If you click on it in the UI Nuke will try to find a plugin, gizmo or tcl proc in the plugin paths and launch it.
You may want to have a peak at the tcl tutorials here to et an idea what you can do via tcl in Nuke.
cheers,
frank