How about the Pickpocket Scanner from Stars? Lets you steal enemy ships' cargo!
Or a Polymorph Beam - changes the target into a random object of the same general size? (Or maybe into a harmless object like Inner Space's Wildcard Defense)
What about area of effect weapons? Would make fleet formation much more important - do you group your fleets tightly to get a quick kill or do you spread out to avoid heavy bombardment missiles?
How about bombs that reduce a planet's value or population/cargo capacity?
Stars also had a device that reduced the speed of all ships in combat by 1/2 square... that shouldn't be too hard to implement in SE4 or SE5...
In a similar vein, MOO2 had a device that reduced all fleets passing near a system to warp 1... maybe there could be a facility and/or component like that in SE5... Interdictor Cruiser anyone?
How about weapons that instead of disrupting the enemy's reload time, merely make it harder for him to hit for a while? (Or target specific sensors... how about a generic "Targets these component families" ability?)
In the same line of thought as area effect weapons, streaming weapons - weapons that can destroy many ships in a straight line or wedge!