For some (myself included), visualizing something is part of memorization. I find constructing diagrams of a system really helps me just get how it works.

So, the OP is probably memorizing the content of the diagram through creating it.

Exactly. The actual creation process helps with memorization considerably. If someone just handed the diagram to me, I'd have a much harder time understanding it.

An untested theory of mine is that this would not be the case if the diagram was more entertaining. If walking through it told a story, possibly in comic-form, maybe with animation, you might have a better chance of grasping it. TV networks do this all the time with animations, most recently with the BP oil spill, showing how it was going to be capped.

FYI you can do the same with pencil/paper. There's no real need to use OmniGraffle/Visio/Photoshop/Whatever (asides from the advantages of having it on a computer).

IMHO, note taking is effective because it incorporates 2 or 3 of the common learning modes: seeing (visual), doing (kinesthetic), and if from a talk, hearing (aural). Generally this is enough to get something in my brain. I rarely need to look at the notes unless they are meeting notes and there is disagreement. For skills, e.g. differential calculus and programming, doing sample problems is especially important.

They are indeed very nice. Does anyone know an application for Linux or Windows (via VM) that is able to create such nice diagrams? I could really benefit from a tool like this but Linux seems to be lacking in this department unfortunately.

Visio is one of the most common apps for Windows that makes similar diagrams, but I really like http://www.gliffy.com and http://www.mindmeister.com. Both are webapps and would work equally good on Windows, Mac OS, or Linux.