One word answer...Point Defense Cannons. Research them fast enough and missiles are pretty much useless where Torps are direct fire and unlike normal beam weapons don't loose damage with range, throw in a Talisman and you rock the enemy
. Best weapons (IMO) are the phased poleron beam (early before phased shields) and the AntiProton beam (mid to late game, good range and damage) followed by the Enveloping Acid Glob (high damage and very nice range). Base se4 the weapons are a little out of balance (IMO of course), but with a good modd this is 'fixed', some of the best (Devnull/P&N) have tonnes of good weapons and counters/defenses against those weapons.