Okay, I've had to think about this one for a while, but now I think I can be confident in my decision now. And personally, I think L has this in the bag for two reasons. One, as has been said before, L is faster, stronger, younger, healthier, and possibly even smarter than John. Plus, his knowledge of martial arts will really help in this fight. John may have a possible durability edge, but that's about it. Second comes in assuming neither character know each other, in which case, L will be able to almost immediately identify him as the Jigsaw killer. In Light's case, he was able to avoid police custody for months, even years, because he was extremely intelligent about what he was doing and made sure to leave as few clues as possible to his whereabouts. As for John, he got raided by the police in the second movie. And not only that, but he made no attempt to hide himself from anyone, even deflecting the term "Jigsaw Killer" as something the media came up with, not him. So, L would be able to identify him, be able to restrain him, and not fall for any mind games he may try to play, such as what happened later during Saw II. Overall, John just couldn't puzzle his way out from this young detective.
Winner: L