Either Dusknoir and his Sableye or Regigigas and his Hitmonlee and Bronzong. Both had many Pokémon so they weren't so easy and short battles, and it was funny when Hitmonlee and Bronzong were hitting us while Regigigas just stood there and tried to move though its Slow Start ability didn't like it.
My favorite boss would have to be a tie between the grand maser of all things bad(because he was hard to beat and because he was funny)or primal dialga(because he was hard to beat and because of the music)
I liked Dusknoir & his Sableyes, but I chose 'Other' because I liked the Lake Trios more (Mesprit, Uxie, Azelf). They were so easy. =P Primal Dialga & Palkia were challenging & hard, and I liked the BGM in the battle. =*