Primarally Phasers or other beam type weapons as they can target specific systems of a starship with controllable damage. Disabling a Starship is more about what systems are damaged and destroyed rather than having a particular weapon (as torpedoes can be used to target Warp Nacelles efectivally disabling Warp drive). Take out the Warp engines and weapons of a ship and its as good as disabled, I can't recall a weapon in canon that’s in common circulation that disables ship systems as its primary function (like ion weapons in Star Wars etc) with the exception of things like the Breen Energy Dampener weapon and a Tholian Web. Dampening field type weapons are the only things I could think of that disable a ship, without physically damaging the ship, but they don’t tend to really exist outside of one off type encounters or local anatomies.
Also the Borg seem to emply a kind of "shield draining" beam but this weapon if it's a seperate weapon at all makes few appearances most notably the Enterprise-D's first engagement with the Borg in which Picard is abducted.Darkseid253 19:46, July 1, 2011 (UTC)