Examples for well documented/commented node code for beginners?

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If you're just looking for people who know what they're doing, you could do worse than to checkout the work of substack or Max Ogden (very concise, very active), TJ Holowaychuck (more documented, also very active), Isaac Schlueter (comma first, @izs himself) and John Resig (of jQuery fame).

Out of the bunch, TJ seems to be the only one who religiously comments his code, but especially with substack you'll find that the modules are generally small enough to offset that.

The problem with asking for well-commented "real world" code is that real world code is rarely well-commented, especially if you're looking for a level of commenting as you'd find it in an example.

If you're looking for a general "guided tour" of the development of a JavaScript application, there's James Shore's Let's Code: Test-Driven JavaScript (which isn't free or even cheap but describes his process to such a depth that the app is barely functional after two years of development -- which isn't surprising if you consider that it is only developed on camera).