CowZ, let me say that if you are new to Visio, it is very easy to use once you've seen how it is used. MS has videos online which do a good job. I'm posting this because I spent way, way too much time making block diagrams in Word at university because I didn't know better.
Not saying that you can't do it in mspaint (you really should get paint.NET if you are using Windows, it is incredible), but you would not likely impress anyone with your work.
You can get the basics of Visio very quickly (drag "shapes" to the worksheet from a "stencil"), move on to using connectors, grouping, and the next thing you know you will be pretty awesome with diagrams. I'm sure Omnigraffle is great, too. I knew a professor who just raved about it, said he used it all the time as an organizational tool (mental scrapbooking, it would seem).
I realize this is the apple forum, but I haven't personally used Omnigraffle. I would recommend Visio on Windows, as it is very, very good at diagrams and flow charts.