I'm not out to be
too nitpicky (or to derail yet another thread), so I'll just say that to me the emphasis on the phrase "martial art" has always been
martial more than art. So -- using my personal definition -- Parkour doesn't quite quality.
Now, this isn't to say it's any less awesome, or any less on-topic for Shadowrun. Parkour's a great way for a shadowrunner to get around, especially given the cyberware, bioware, and magic that can make them very, very, good at it. It's a great way for a shooter to get into position, get out of position, etc, etc -- so martial characters can certainly
use it, but I see it mostly as being in preparation for, or to escape from, an ambush site or something else. I've dug "Mobility Adepts" for kind of a while, folks may recall:
http://forums.dumpshock.com/index.php?act=ST&f=7&t=11661&st=0#entry354346 
And, given the abstract nature of Shadowrun's Martial Arts qualities (re:
Arsenal), I'm not horribly opposed to some athletics (rather than unarmed combat) oriented "Parkour" qualities being cooked up, that help modify running speed or jumping distance or falling damage, that could be priced and categorized similarly to the existing Martial Arts qualities. So I don't mind it being lumped in with "martial arts" in a Shadowrun house rules sense, where those qualities are concerned.
I just...don't consider it a martial art, in the literal senses with which the words are used.
Okay. There. I said my pedantic bit, and we can get back to talking about serious business like crime-fighter vigilante Shadowrunners.