In the dojo fight, while Morpheus is trying to 'free his mind' it goes into the fighting too. I anylized the entire dojo fight sequence and I believe I can see what arts they use and when.
Throughout the fight Morpheus uses a mix of all the styles he's learned, it looks like, and I couldn't tell any specifics from him. Neo however...
When it begins, right after they enter the sparring program, Neo starts off using Karate. Morpheus kicks his *** with that, and they pause to get into another fighting stance. Neo assumes one of Jeet Kune Do, (I know there isn't a SET stance for JKD but it was the stance that is the most common) with two fingers extended and his hands slightly moving. Morpheus kicks his *** again, so Neo switches styles. Next, he assumes a Tae Kwon Do stance, and does a little better but still gets pummeled. The next pause they go into, Neo doesn't use any stance, and starts punching sloppily. I can only assume that this was the drunken boxing. He gets creamed really fast with that, and goes into what looks like a Kenpo stance. Neo is again beaten with that. The next one, Neo assumes a Kung Fu stance, I think, and then after that he uses sort of a mix of styles like Morpheus does, but he still leans toward Kung Fu. He is using a full mix when he defeats Morpheus, and it is then that Neo has learned to 'free his mind' from using one style of fighting.
That's my take on the fight at least. If you believe I was wrong about anything, as these were only guesses, please tell me.