I use Visio because it's easy. I also use it because I have an ancient version (before it became MICROSOFT Visio) that came free with a computer purchase (back in the 90's... an "Acer" computer that my parents bought me towards the end of college). I kept the "freeware" CD, even though the computer is long gone, and load it onto every computer.
Granted the process of getting it into a clean form is a bit of a pain (from the old Visio format to an Adobe Acrobat .pdf (using Adobe Acrobat full version as a "printer"), then to the .eps form excepted in LaTex and cropped with The Gimp (or another image editing program... but I have the procedure written in a lab notebook.., and once I knew the procedure, my diagrams always looked clean.. and Visio made GREAT diagrams easily with a drop and drag kind of feature, and has a grid to align things well). The new Microsoft Visio does (I believe) have better options of how to save the images... but I only used a friends once... it's pricey!
For graphs (plotting data) I have used either "Igor" or "Origin"... I prefer Origin (note.. it is more pricey than Igor, which at least used to have a cheaper student/academic version). There may be file conversion subtleties there too.