What are the most popular packages used to create graphs for astronomy journal papers? Looking at various journals, the styles of the graphs appear to be quite uniform but I can't identify the package(s) that create them.
The most commonly used packages for generating graphics in astronomy are probably
IDL -- this has long been the most popular, in part because there is a lot of astronomical data reduction and analysis code written in IDL.
The Python package matplotlib
The apparently uniform style you refer to is probably a historical combination of IDL and SuperMongo.
Matplotlib (and other Python packages that act as wrappers around it) is on a trajectory to displace the others; I strongly suspect it is already much more common than SuperMongo, and may be roughly as common as IDL by now.
You will sometimes see figures produced by the PLplot library as output from programs written in Fortran, C/C++, etc. Plots produced using R are also starting to appear.