Graphviz is fantastic. I'm pretty sure you can still read your .dot files into OmniGraffle (for when you need to add a lot of color and annotations). I also think its power comes from being to be turned into a callable library useful in several other languages (python). Also I can't imagine using a service that hosts my private data in order to build a layout... but maybe that's just me.

Two other alternatives: The best one for network-bounce / sequence diagrams.. great for when you need to explain all the bounces in your mulit-tiered web app https://www.websequencediagrams.com/ and http://sverweij.github.io/mscgen_js/