Elder Princess Shroob for me. No save after the previous fight and then her! My hands hurt so badly after all that. It was much easier my next time through when I got the best equips and abused badges and items to rain down madness on her!
Shadow Queen probably the only time I died in any of these games, I kinda did against Elder Shoob Queen (I know it said Princess I see her as the queen). Also Shadow queen as the most experience in and out of the game. There is no way to timed that storm as she appeared and stopped after here death...just perfect!