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Pros
Pro Cross-platform
YUIDoc is not available for JavaScript only, it supports every language that has /**/
comment blocks.
Pro Great output
YUIDoc's default theme is very appealing. The output it renders is very readable, searchable and user-friendly.
Pro Live preview
A standalone doc server is included which allows you to easily preview the documentation as it's being written.
Cons
Con The name of the method/class need to be mentioned in the comments
Since YuiDoc only parses comment blocks, it requires the names of the methods to be specified there, ignoring what's outside of the comment block.