I had been using Origin to generate plots mostly because that's what my adviser used. I absolutely despise Origin. I complain that I expect things to "just work." Origin caused me so many headaches during my Master's thesis that I was desperate to find another option.
I found Graphpad. I've been messing around with the trial (nothing good is ever free) and have decided it is superior for a few simple reasons. First it integrates Mathtype so i can guarantee the size of my fonts are always consistent. In Origin you had to copy in Mathtype as images and resize inside Origin, but the point size differed if it had subscripts or superscripts. There is an "align" option in Graphpad that guarentees alignment of axis in the final result. This is also useful for inset plots or denoting graph a, b, c,...etc. and making sure that everything lines up correctly.
Also origin would leave large white areas around the outside of the plot unless you changed the preferences. Importing a plot made with someone elses settings would almost always screw things up. Importing to Word was also a nightmare with crashes, but mostly with alignment problems. Graphpad has a layout feature that builds the final plot for you. For instance if I want two plots side by side, I just go to that layout and drag and drop the previously (automatically) generated plots into the placeholders.
If you have multiple plots that you want to ensure are identical in format, there's a magic want tool for that. It's not more than 3 clicks. If you are importing data from multiple files or only certain columns or rows, the filter tab has everything you need. You can view EVERYTHING before it is generated - the data before it's imported or the graphs before they are formatted.
Origin is more powerful. Graphpad appears to be made for business rather than science. It can't do 3D plots or some of the other fancy things Origin can do, but for simplicity, predictability, intuitive design, and repeatability Graphpad is superior by far. Consider that I went from downloading the trial to figuring out how to set up preferences to importing data to generating professional high quality graphs in about an hour with Graphpad. I've been using Origin for over 4 years and still haven't figured out ways around the problems I've faced.
These are the Preferences i use for scientific plots
frame -no frame
Default color scheme black and white
main -regular times 14
axis titles -regular times 12
numbering -regular times 12
legend -regular times 12
SYMBOLS AND LINES
line thickness -1/2pt