I was fond of dia when it popped up but I don't think its been developed since 2009, and does not produce automated layouts.
Just tested yEd, the 3.22 zip does not seem to be available (though I might just have looked in the wrong spot), however the 3.23.1.zip works perfectly (just make a port with updated distinfo and Makefile). They're using a AI database to rearrange layouts, so at least the 'free' version requires you give feedback whether you think the automated layout is good or bad. In exchange it looks to handle quite complex diagrams, use their "one click layout" tool to have it rearrange the layout so connectors don't need to cross each other, looks cute.