what exactly does it mean when brilliant weapons (like the sword +5 you get from battle square I think) are said to have brilliant energy:"attacks ignore target's shield and armor bonuses"? does this mean you roll against the target's natural AC ? what if the target has magically enahnced AC (shield,cat's grace,haste etc.)?

Yep, shield bonus means AC bonus from shields and armor bonus means AC bonus from armors. So, all spells and items that give deflection, natural armor, dexterity or some other bonus still apply.

thanks Harkle, brilliant speed...

No problem :) Glad to be help.