Ahhh... Martial arts movies. I'll limit myself to a few that feature the best martial arts fighting scenes, regardless of story or acting or anything else (you can find all that stuff on any movie web site)...
Dragon Inn. Brigitte Lin, Maggie Cheung, Tony Leung. 2000, dir. Raymond Lin.
District B-13. Cyril Raffaelli, David Bell. 2004, dir. Pierre Morel. In addition to fantastic martial arts choreography, the film features some amazing
parkour. My Father is a Hero (aka Jet Li's The Enforcer). Jet Li, Anita Mui, Miu Tse. 1995, dir. Corey Yuen. One of the highlights of this film is 11-year-old Wu Shu phenom Tse.
Kiss of the Dragon and Romeo Must Die. Both Jet Li, with Brigitte Fonda and Tcheky Karyo, and Aaliyah, Isaiah Washington, and Russell Wong, respectively. 2001 and 2000, dir. Chris Nahon and Andrzej Bartkowiak. Some Li purists dismiss his Western films out of hand, but I think these two are often underrated. The fight scenes between Li and the aforementioned Raffaelli and Wong are great fun.
The Rundown. Dwayne "The Rock" Johnson, Sean William Scott, Rosario Dawson. 2003, dir. Peter Berg. This is really one of the best
action movies of the last ten years, and wouldn't normally qualify as a "martial arts" film, except for the fantastic fight scene between 6'4" Johnson and 5'5" Ernie Reyes Jr.
The Bourne Identity, The Bourne Supremacy, and The Bourne Ultimatum. Matt Damon, et al. 2002, 2004, 2007, dir. Doug Liman, Paul Greengrass. Again, not really "martial arts" movies as much as action films, but each features one excellent, set-piece throw-down. Contrasted with more traditional martial art films, the fights aren't designed to be pretty, they're designed to look like two commandos stripped of their guns trying to kill each other however they can. A ball-point pen. A telephone. A book. Wu Xia this ain't.
Posted by Rush
Marked for Death - Some of Segal's best on-screen aikido IMO
Only the Strong - capoeira baby

These two films are also on my list. Both are pretty bad, as movies go, but
Aikido and
Capoeira are fun forms, and you won't find them in many movies. If you ever get a chance to watch Capoeiristas or Aikido practitioners in person, I recommend it.
Steven Segal is a disaster as an actor, but the way he does Aikido, it's easy to imagine how the Japanese samurai would've kicked your ass even without their swords.
A random side note, Mark Dacascos - the lead in
Only the Strong - is the host of the television show
Iron Chef America.