I always liked to use torpedoes, but was disappointed with the way SE IV treated them with limited range. So - BAM - I added some range and just a smidge more destrutive power...
I don't like missiles all that much - they become really ineffective against an opponent with good point defense.
Once component that I modded in to the game is Pulse Phasers. They're like souped up Meson BLasters and quite effective at close to mid range.
------------------
Visit the Spoogy Federation at:
http://spoogyfederation.tripod.com