I am assuming that the EDU version of the segger J-link is the same as the commercial version - they just sell it at very low price for students/instructors. I think this is indeed the case. The IAR J-link tool (yellow box) is the same as the equivalent Segger J-link tool (black box) inside and I have used both/either interchangeably on projects.
Depending upon what processor your are using in your project you can have additional features supported with the tool and the IAR toolset. For example, if using NXP LPC21xx processors (among others) you have the "unlimited flash breakpoints" capability in your code for improved debugging.
I think that the toolchain is quite good.