The SVG format is the Grand Central Station of vector graphics, with junctions to PDF or and the other compatible formats like as Adobe Illustrator, EPS and xfig.
pdf2svg is handy used in conjunction with (almost) any of the other programs to convert between formats.
Open source Inkscape can do everything, although I find its Adobe Illustrator pretensions (perhaps unfairly) grating. Aimed firstly at general vector graphic design, which means the functions you want for sciency stuff are not front-and-center, but it can be done.
A fresh option leveraging web technology is Jarosław Foksa’s Boxy. (web app with pseudo-desktop apps for various platforms.) I think it is free, but closed source?