Brazilian Jiu-Jitsu Versus Japanese Jiu-Jitsu

Which is better for self-defence, Japanese or Brazilian Jiu-Jitsu?

These are both fine styles, and while I am trained in a Japanese style of Jiu-Jitsu I have taken a handful of classes in Brazilian Jiu-Jitsu, attended a seminars, read the books, and followed the buzz.

In this comparison I say go for instructor and school over style.

Look for:
Safety in training
Technical excellence
Skilled and well-behaved students
Good training atmosphere
An emphasis that fits your goals
No lock-in contracts
An experienced martial arts practitioner is going to be in a better position to be discerning than a complete new-comer.

Some more on emphasis. Consider:
Self-defense vs sport
What are the main areas of technique that you are training?
Balance between drills (kata) and free practice (randori)
These factors vary from style-to-style and instructor to instructor.

The broad technical areas in martial arts are striking techniques, throwing techniques, standing grappling techniques, groundwork techniques, and weapons.

Japanese Jiu-Jitsu

In the style of jiu-jitsu that I practice the main areas of emphasis are throwing, groundwork, and standing grappling (what we call restraint and control). Striking is there from the outset, but has less emphasis, and weapons enter later. I personally emphasise the self-defence and health aspects, with a little competition for fun and stress-testing, but not an aim in-itself. We do mainly drills, with a little free practice. If we are optimized for one thing, it's general self-defence.

Because there were many styles of Japanese Jiu-Jitsu -- not to mention the "reconstituted" styles -- technical emphasis and training methods will vary from school-to-school.

Brazilian Jiu-Jitsu

In Brazilian Jiu-Jitsu the main emphasis is going to be on groundwork, because that's their speciality. So if you opt for Brazilian Jiu-Jitsu you can expect to get good at ground-work comparatively quickly, while development in other areas seem to be taught later, if at all. Sports / self-defence seems to vary between instructors, but since they are into no-holds-barred, my primary concern would be about safety-in-training. Expect lots of free practice, but this may vary between instructors.

While it is true that a Brazilian Jiu-Jitsu practitioner can bring a fight to the ground, in self-defense against multiple attackers you need to keep your feet to escape. You may need to look for a school that teaches a separate class in self-defense to complement the usual classes. The Royce and Charles Gracie book Brazilian Jiu-Jitsu Self-defense Techniques shows what to look for (and the techniques shown look very familiar to anyone schooled in the Japanese techniques).

Conclusion

Instructor and school over brand. Talk to the instructor, ask around, see if you can try out a sample class. If you can find an "old-timer" who has been teaching for more than -- say -- 25 years, (s)he should have a good perspective on all these issues.