Shinsetsu explained this quite well.
Just as he said, if you want to add any in-game bonuses for learning specific styles, you're making up house rules... however, it would be a lot of work to make up 'accurate' prestige classes and rules for new martial arts styles. You could look at the Drunken Master PrC in Sword and Fist for a start, but I personally dislike that prestige class - it's pretty wacky and brings up all sorts of weird rules questions in-play. It's also fiendishly stereotypical, which often offends martial arts purists.
One easy solution (which wouldn't take all that much work) might be to write up a few new 'feats' which would represent mastery (or at least significant ability) in a specific martial art - the feat would provide a few minor bonuses that would reflect the *cinematic* benefits/specialties of the martial art in question, basically, make enough of a difference to let the player feel like his/her character has learned something special. Full-blown prestige classes would require you to do a great deal of research, since movies and games are nice for inspiration but often do not strive to be accurate.
Accuracy would be difficult to ensure - certainly, most martial arts are at a disadvantage against an armed opponent - if this were not true, most martial arts would not bother with instruction in the use of weapons, but wushu, karate, penjak silat, escrima, etc. all make a point of using weapons when available. (I know some grappling-centered martial artists who can get pretty macho about their ability to deal with their opponents. "If I need to, I can just suck up one of your kicks or punches, and then I can move in and pin you." I usually shrug and say "Well, if you can suck up a sword strike and still pin me, then you deserve to win.")
So I say, don't worry about accuracy - a single feat, summing up the best cinematic advantage of the martial art in question, would be sufficient for play. The feat could have prerequisites that reflect the basic training/foundation of a style, demonstrating the character's previous devotion and study to the martial art, and then the feat finishes up the bonuses.
Here's a few possible examples: (PS: I only practice a few martial arts myself, and I wouldn't necessarily call myself an expert in any of them - so anyone who wants to nail me to the wall for 'butchering' the representation is more than welcome to offer criticism.) I've tried to make them useful and desirable, without being off-the-wall. The prerequisites also (hopefully) keep these from being no-brainer choices, making them something of a commitment to character flavor.
Feat: Karate
Prerequisites: Improved Unarmed Strike, Weapon Focus: Unarmed Strike, Power Attack, Proficiency in Staff, Nunchaku, Kama, or Tonfa (stats same as Nunchaku)
Description: You have attained significant skill in a traditional hard style of martial arts. You gain an additional +1 to damage with your unarmed strikes, as well as with one of the weapons listed in the feat prerequisites.
Feat: Muay Thai
Prerequisites: Improved Unarmed Strike, Weapon Focus: Unarmed Strike, Toughness
Description: This martial art style emphasizes powerful strikes, close-quarter combat, and the ability to withstand and endure pain. The body is conditioned to give and take, in a brutal and very effective way. You gain Damage Resistance 2 against unarmed attacks and subdual damage. You also get a +2 to your saving throws against any effects which rely on pain, such as Pain Touch, Symbol of Pain, etc.
Feat: Judo
Prerequisites: Improved Unarmed Strike, Improved Trip, 5 ranks in Tumble, 5 ranks in Escape Artist
Description: This martial art specializes in close-quarter combat, spending less time on striking techniques and more time on pins and grapples, within the effective range of most other martial arts. You gain a +1 to touch attacks and grapple checks, and a +1 competence bonus to opposed Str/Dex checks when Tripping an opponent, or when he/she is attempting to Trip you.
Feat: Tae Kwon Do
Prerequisites: Improved Unarmed Strike, Circle Kick, Dodge, 5 ranks in Jump
Description: Relying on fast and powerful kicks, this style also includes a number of flashy aerial techniques. What is sometimes forgotten by the layman is this style's emphasis on footwork and strategy. You can use Circle Kick when executing a Standard Attack (the original feat requires the use of a full-round action). Your Dodge feat is also upgraded, giving you a +2 dodge bonus to AC instead of a +1.
Feat: Twin Jian
Prerequisites: Two-Weapon Fighting, Weapon Finesse: Jian, Weapon Focus: Jian (longsword or rapier, depending on era and taste)
Description: You have spent a lot of time learning a difficult double sword style. Your penalties for two-weapon combat are reduced by one. (i.e. you have -3/-7 to hit (primary/off-hand) instead of the usual -4/-8 to hit, for using two medium-size weapons. Ambidexterity would change the penalties to -3/-3 (primary/off-hand))