In practical terms? The 3.6 GHz machine is about twelve percent faster at the base clock speed, offers Turbo Boost (where the CPU shuts down unused cores to boost the speed of the active ones - in this case, up to 3.86 GHz), and will suit anyone who needs high processor speeds very well.
Other than that, the machines are identical in terms of RAM, HDD, GPU, and so on. Go for the i5 if your programs like a speedy CPU, and if they don't really need one, the i3 is more than sufficient.
Is 12% considered a lot