Personally, I'm playing a game where *I* don't use missiles at all. I haven't met any aliens yet, but I'm building my defenses for them. Much of my defense revolves around CIWS and gauss cannons, since I know they'll be using missiles galore. On every dedicated anti-missile ship I'm putting numerous quad gauss cannons with as much accuracy as possible. Every single ship of mine also has CIWS, even the escorts.
I even gave one of my commercial troop transports over a dozen CIWS. . XD
Most of my ships' offensive capabilties currently revolve around gauss cannons as well, although I plan on implimenting a strong boarding party strategy.
Once I find some enemies, I'll let you guys know how everything fares. SPACE VIKINGS, HO!