Wow, I have seen both and I have thoroughly enjoyed both. However, they are two completely different movies. Most of you say, "But archer, how can you say this, they are both revenge movies!" Not at all true. The Punisher is a punishment movie
and Man on Fire is a revenge movie. In all seriousness though, Man on Fire is very plot and character development driven, and it deals with themes such as self-sacrifice, love for life and other human beings, etc. The relationship that develops between Pita and Creasy is one that you sense is very true and believable (partially because Man on Fire is based on a true story). Tony Scott does a great job with this film.
On to The Punisher. If someone who weren't into the epics of Frank Castle in the Marvel Universe, then they would probably say that The Punisher is inferior to Man on Fire. I disagree, because, as I've said before, they are two different films and it's like comparing apples and oranges. The Punisher follows the sense of the comic books very well, Tom Jane is ideally suited for this role, he isn't a pretty boy and he can kick your ass. The scenes with the mafia bosses the Saints are laughable, but this is the way they would be portrayed in the comics, so I have no problem with it. For fun factor, The Punisher is definitely better, you just don't get much better lines than the one where Castle kills the last Saint brother. For in-depth introspection into movies, then Man on Fire is definitely better. It really depends on your mood, because all action lovers will enjoy both films, but for the casual goer, it will depend heavily on what you feel like watching at the time.