AeroDataUSA
One system I've used at several airlines, from D328s to B757s is called Aerodata.
It interfaces with your flight planning system, and calculates from the flow equations in the AFM the most exact weights available, and it also has a W&B system as well.
It isnt cheap - they maintain the performances and obstacle databases. Includes engine-out departure procedures for those airports where required. It calculates under US FAR 25 however, I dont know if it does the JAR rules.
PM me if youd like more details - I have a PDF from them somewhere on here.