Karate!!! It's tha best xD.

I've always been a fan of Tae Kwon Do and have been doing it for the past 2 years myself.

Judo
 

I do judo in Brazil! In my opinion, it's the best, since you need strengh as much as brain!

Alot of the modern Martial arts. I.E. Krav Maga and the System
are very good. they have taken the best from other martial arts and put them all together....

however THE best martial art by far...is Southern Mantis...its still a bit secretive so hard to find a teacher, but people that know this style can take serios blows without coming to harm (like the monks) and can shatter bones with a single blow, without putting in effort

Also Karate is a derivite of Tiger style...

Any form of Shaolin.

unfortunatly most of the shaolin styles have been lost.

the chinese comunist party axed the temple...then re-opened it many years later...as a result several monks went to USA etc.

also Many styles were lost when the temple was burnt down in the old day's.
only 5 monks escaped,

You cant say one MA is better then another one. But If I have to choose, Karate.

Muay Thai, some BJJ and wrestling and you're good to go.

Tai Chi ...
 

For me, i tried at least 5 or 6 art forms, but Tai Chi is more spiritual.
It's a mind body thing.

My guess, if you want to become better at any MA, practice Tai Chi and it will improve your style, speed and elegance.

I also practice Brazilian Capoeira, does anyone know about any Dojo's in Tokyo?
Judging by the amount of Brasillero (Brasil people) in Japan there must be a few.