If you want a diagram you can embed in text and check into source control, take a look at GraphViz. <a href="http://www.graphviz.org/" rel="nofollow">http://www.graphviz.org/</a><p>You can even embed it in other things, like Wikis. <a href="https://www.mediawiki.org/wiki/Extension:GraphViz" rel="nofollow">https://www.mediawiki.org/wiki/Extension:GraphViz</a>
Microsoft Word and PowerPoint.<p>Sometimes Excel when diagram could be made by drawing borders around cells and resizing rows and columns as per need. This helps when unplanned non-linear horizontal and vertical scaling is needed while making the diagram.<p>The SmartArt concept they introduced was quite promising, though I find the current state of it lagging. I am sad that it never picked up.
I had started with using MS Visio at my job.
Though I had absolutely no experience in making diagrams, Visio was quite easy to get started and become comfortable in quick time.<p>The downside of course is that it is not free.<p>I would also like to know open source alternatives to MS Visio. I can see that Ubuntu 12.04 comes with Libre Draw, but I haven't tried it yet.
LibreOffice Draw is reasonable if you are coming from Linux.<p>Otherwise there is GIMP too.<p>+1 to all the other open source solutions mentioned here.