OOk enough with the thread derailment..
Legitimate Japanese jujutsu will usually include weapons training (generally short and long swords, occasionally other stuff like spears, staff, and other traditional edo period weapons), kyusho (weak points), a very large variety of joint locks, standing and ground grappling, chokes of various kinds and reiho (proper manners). Also taught at ALL Japanese jujutsu dojo are proper breakfalls, which are unfortunately severely neglected in many other arts.
Most Japanese jujutsu is taught standing up and generally relies on a combination of hitting a weak point and breaking balance simultaneously to defeat an attacker. Make no mistake, you could be 3 feet tall and facing a 6foot tall opponent, if you know your jujutsu properly you will be able to defeat your opponent without too much trouble.
BJJ is geared towards fighting while on the ground. The workouts tend to be a little more strenuous than most Japanese jujutsu places. I've found in my area that the practicioners are usually of very good quality but often have poor manners. Maybe they should get a Japanese guy in there for some reiho training
Either way you can't really go wrong but take a close look at why you are going to learn jujutsu. Brazilian jujutsu is very good for ground fighting by itself, but if you want it purely for self defense it's important to learn some standup along with it, or do mixed martial arts so you aren't relying on your ground game alone.