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Pros
Pro Numerous templates available
The community behind JSDoc has built sever templates and other related tools that allow you to use JSDoc in a simpler and more efficient way.
Pro Grunt plugin available
For people who like to use Grunt, there's a Grunt plugin available.
Cons
Con Only provides an output of the API
JSDoc only provides a linear output of the API and not really a visually appealing or any information other than the methods and what they do. It's very technical so it may be hard for beginners to read documentation generated by it and understand it.