In Meteor 0.5.4 this has become a lot easier:
First run the following commands from the terminal:
npm install -g node-inspector node-inspector & export NODE_OPTIONS='--debug-brk' meteor
And then open
http://localhost:8080 in your browser to view the node-inspector console.
Since Meteor 1.0 you can just type
which is essentially a shortcut for the above commands, and then launch node inspector in your browser as mentioned.
In Meteor 1.0.2 a console or shell has been added. It may come in handy to output variables and run commands on the server: