Smash makes the most money by far as far as fighting games are concerned. Alphazealot pretty much laid down the facts on that.
After that would be DoA4 which receives sponsorships and is in WCG/CPL/CGI, all of which reward about $10,000/$5,000/$1,000.
After that I would say a toss up between Marvel and 3rd Strike. Leaning more toward Marvel as that community has a tendency to really heat up in money matches.
The majority of other fighting games are usually unprofitable, sometimes even to the winners.
If you are playing fighting games you must come to term with the fact that they are severely unprofitable unless you are a very good Smash player (which I mean VERY GOOD) or one of the 8 “choosen” DoA players that get to go on TV, look like idiots, and get a nice fatty check at the end of the day.
Fighting games are to competitive gaming as Folk Style Wrestling is to competitve sports. It’s a truely involving, skillful, and amazing activity. However it is woefully unpopular and never expect to get a paycheck for it.