It all depends on what role you want them to fill. If you have hammerheads and broadsides (and maybe fusion piranhas) to deal with heavy armor, you be a little more flexible with your CS. From what I have read and playtested, CS fall into two camps (close and long range support). Plasma fulfill both (and cost the most consequently).
Long = Missile pods, plasma
Close = TL Flamer, plasma, or fusion (flamer is always equipped twinlinked to reroll wounds)
If you want to frag MEQ and MC and feel comfortable that you can handle heavy armor with other units, I would go with plasma and missile with multitracker. You invest in volume of fire and not quality of fire. You can always throw in a unit of pathfinders to give you that +1BS if you can't live without it. After all, you only get to take 9 of the suckers, so you might as well pack as many guns on them as you can. I always liked:
3 CS: Missile pod, Plasma, multitracker, bonded, HW drone control w/ 2 shield drones, HW Target lock
3 CS: Missile pod, Plasma, multitracker, bonded, HW drone control w/ 2 shield drones, HW target lock
3 CS: Twinlinked flamer, fusion gun, bonded, HW drone control w/ 2 shield drones, HW target lock