From what I've read up on these two combative arts, they're similar, but very different. JuJutsu (JJJ) is more of a no-rule self-defense system. Anything is allowed, even biting, eye-gouging, hair-pulling, and stuff like that. JJJ practitioners focus on throws and some standard stand-up techniques, as well as some ground work. It's pretty balanced out, so you don't do particulary well in a particular situation. This could be a good and bad thing. Depends on the situation.
BJJ is a lot more focused on ground work. Some schools teach basic stand-up, but some don't. I think they don't focus on throws too much (maybe not at all). A lot of their joint locks are much more dangerous (or so I've heard) than those of JuJutsu's. It's more compatable with MMA, because it's all about submissions and your position on the ground, while JJJ is all about real combat.
That's the basic differences, to my understanding. I could be totally wrong though, lol. Hope I helped.