I personally love heatseekers. They sometimes miss when the target flips toward me suddenly, but most times they work just the same as an IR missile.
Plus they have a bigger warhead.
My least favorite weapons...
Pilum Friend or Foe - Its got the smallest warhead of any of the regular missiles, it has a habit of not targeting the ship I'd like it to target, and the IR missile lock doesn't take long enough to make much of a difference.
Rocket Pods (not dumbfire missiles, which have a bigger warhead, and are fun to use at point-blank) - itty bitty warheads, just common enough to make you want to use them at medium range, and the Nephilim have a bad habit of turning to one side the instant I fire one.
That stupid torpedo that I fired right when the targetted cap ship blew up, and that continued to circle endlessly until a friendly confed fighter flew into it, blew up, and got me in trouble as a 'traitor' (this was a mission in SOP).