I do like an ion cannon from time to time. Can be good on a fast frigate that can hit behind the enemy shields on occasion but do not have enough power to outright kill them then and there.
It can be hard for me to justify an Ion Beam though, I would be giving up a medium energy in exchange for 200 flux/second, and beams generally do not go with driving up hard flux on a ship platform. Eagle/Falcon perhaps. Conquest also. I don't use those ships often.
Xyphos have always interested me with their 1200 range Ion Beams, especially in 0.91 when one of my carriers could sometimes tell theirs to escort my SO flagship, but in 0.95, fighters are expensive to deploy, a lot more vulnerable, and enemy broadswords are far more of a priority than EMPing exposed the armor/hull that I'm dumping assault chainguns and possibly missiles into.
So for short range EMP, ion cannon at 50 flux/second or Sabots are excellent, and for long range, secondary EMP from Tachyon Lance. Ion beam, not sure where it would fit generally, maybe one of the medium slots on an Eagle, but aside from EMP it's 200 flux/second for 50 energy damage.
There's also the Ion Pulser and the new omega weapon. Ion pulser could be good with hit and run on certain phase ships and the Hyperion, especially when the shield can be bypassed to EMP or if something else has cracked the armor, but if there's a small energy slot for an ion cannon, I would use the medium energy for something else.