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Pro Built-in diagramming
Pencil allows you to create diagrams and flowcharts directly in its editing software. No other major mockup editor allows you to do this so easily, and doing so usually requires the use of separate software.
Pro Versatile outputs
Pencil includes the standard outputs that all mockup editors should have. It is notable that the program includes HTML output to "Single web page", which is a rarity among wireframing programs.
Pro Free open source software
Free and Open Source
Pro Linking, even in HTML
Like Balsamiq, Pencil allows you to link multiple wireframes together within a mockup. More importantly, this linking is preserved when the mockup is exported as HTML, allowing you to create a full "web site" mockup with numerous pages.
Pro Vector icons
Similar to open-sourced UI libraries, Pencil also includes open-sourced clipart that allows users to drag-and-drop a seemingly unlimited collection of clipart into wireframes.
More importantly, these icons are all vector format, thus they are fully scalable.
Pro Immense shape database
Unlike other tools which may include just a small collection of shapes to put in your wireframe, Pencil has a huge, well-organized collection of shapes and flowchart elements.
Most notably, Pencil features an iOS and Android collection with all common UI shapes to make mobile wireframing a breeze.
In addition, Pencil allows drag-and-drop installation of user-created shapes, a rare feature in mockup tools.