WebStorm is the only IDE with native Meteor server code debugging support - check out this video . Even on Windows, debugging is very simple:
WebStorm 9+
Go to Run -> Debug -> Edit configuration ..., click the plus sign, click "Meteor". You can add an environment variable such as ROOT_URL if you need to.
WebStorm over 9
This answer is retained for historical purposes only. You should update WebStorm.
In older WebStorms, you had to create a Node.js debug configuration.
on the server, export the NODE_OPTIONS=--debug=47977 environment variable. For example,
NODE_OPTIONS=--debug=47977 meteor
Create a WebStorm / PhpStorm launch / debug configuration using the port above (47977) and the server host. Leave 127.0.0.1 if you are debugging locally.

- in WebStorm, Run -> Debug <myapp>, or press Shift + F9. Make sure you see "Connected to <your host>" in the Debug panel
Now you can set breakpoints, access local variables, etc.
To debug the client, simply use the Chrome or Firebug debugger.
Troubleshooting
Process disconnected unexpectedly - this happens when a meteorite starts automatically due to the lack of specific support for the Meteor. Just run -> Debug <myapp>, or press Shift + F9 again.
you cannot connect to the server - make sure that the firewall rules allow incoming connections to any port that you selected for the Node.js debugger (47977 here).
Dan Dascalescu Feb 05 '14 at 7:36 2014-02-05 07:36
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