As far as i'm concerned, the best groove for joe is K, though popular opinion is that A is best, i will write what i usually do when using K.
Joe has 3 supers:
qcfX2 P: joe throws a single tornado that rises to the top of the screen and travels almost all the way across the screen. This super is good for catching low jumpers.
qcbX2 P: joe raises both arms and creates 2 giant cyclones above his head and around his body. This super does great damage and is great if someone is dumb enough to jump in. If for some reason you are going to wake up super, this is the one to go with.
qcf, hcb, P: An auto combo super, Joe starts with hundred hands, throws a pair of tornados, raises the opponent with a tiger knee, and brings it down with a flip kick. I don't really use this super too often, so if anyone does, they can give you the goods.
Joes specials:
Hundred hands: Any punch button X 5: Similar to Hondas hand slaps, this is probably joes best special. Mainly used if baku cancelled.
How to Baku cancel: The baku cancel basically cancels the hp version of the hand slaps and gives you a great frame advantage, allowing you to link previously unlinkable things, like the slide{down+hk} or trap the opponent in the corner forcing them to block. You must use the hp version of the move, and to cancel, you must hit the HP and LP buttons twice, after the first hit of the punches connects and before the second connects.
Cyclones: Hcf, P: Joes fireball, the lp version throws a single tornado that travels half screen, the mp throws 2 tornados half screen, and the hp throws 2, full screen. These are great, the lp recovers very quickly. Mix these up and try and get your opponent to jump over one and into you knee or super. Be careful, these are highly punishable.
Tiger Knee: Dp, K: Pretty good dp, the hk version has much invincibility. and the lk version is very fast, think kens lp dp, but not quite that good.
Flip kick: Qcb, K: Joe does a flip kick, eats opponents up in the air, but highly punishable on the ground. The mk version is a really bootleg crossup.
Sex Kick: Hcf, K: Useless, only use to cover ground.
Joes best pokes:
S.Hk: Pretty good poke, long range.
S.Lk: Annoying and quick.
C.Lk: Good and fast
C.Hk: The slide, Great and fast, great range and is a good punisher.
C.Lp: I mash this when the opponent is waking up, they get hit by a couple of jabs and that combos into the hands. After the first couple of times, i stop so they try and dp me and than i can combo them when they land.
Joe should never jump really, but if for some reason, you do, use jumping mk.
Joes main game:
Footsies are obviously joes style of choice. Joe doesn't have many combos, you pretty much have to go poke for poke, try and fill that screen with safe typhoons. Dp their pokes, and stay out of the air. Also the baku cancel is very important.