When comparing yEd vs Pencil Project, the Slant community recommends yEd for most people. In the question“What are the best flowchart / diagram softwares?” yEd is ranked 8th while Pencil Project is ranked 10th.
Ranked in these QuestionsQuestion Ranking
Pro Completely free
Runs on Windows, Linux and Mac OSX. There also is a Web application.
Pro Automatic Layout
With automatic layout you get great looking diagrams with very little effort. yEd has the most versatile and most complete collection of automatic layout algorithms.
Pro Pencil Project as a Firefox extension
Pro Inter-page linking
Con Not free-as-in-freedom
Not released under an open-source license.