[widdma]

I'd second the PGFPlots recommendation. Easy to create plots by hand or you can use matlab2tikz (mentioned but dismissed in the article) if you're coming from matlab.

I'd also second the latexmk recommendation!

[tjl]

I love matlab2tikz. I used it for all my plots in my Ph.D. thesis (and I had a lot). I also really like latexmk.

For non-plots I love Sketch (http://sketch4latex.sourceforge.net) which is pretty great for doing diagrams with 3D objects, especially if you use the sketch-lib (https://alexdu.github.io/sketch-lib/) which provides a bunch of useful simple objects to manipulate.