Out of those two, I felt Batman Begins was better. It was great as an origins story and had a great cast. Spider-Man, I felt was great in handling the origin of Spider-Man, but where it falls flat is with the casting, in my opinion.
BB is a master piece IMO. Perfect cast, amazing cinematography, great story, slick dialogue... it's 97% perfect, the 3% missing is slightly poor fighting sequences (specifically the hand to hand fights). BB smokes the IM even worst.