One thing I've heard of is the car going into some sort of sleep mode if there has been a long period of inactivity in order to conserve the battery (five days). The key-less entry system disables itself. Apparently you need to unlock the doors manually and then try the key fobs again. I've heard that usually works. It happened to me once after a vacation, so I unlocked the car manually. Afterward, the key fobs worked normally.
Another thing is that these cars are infamous for not being to arm or disarm the alarm from greater than about four feet away. I'm not kidding. There is a fix that you can do at home that basically removes some unnecessary shielding from around the antennae wire in the drivers side A-pillar. Do a search on the Rennlist 996 forum and you should find a link to an article that shows you how to fix that problem. I bookmarked it but haven't actually taken care of the issue yet. Here's a link to a thread that should lead you to the article.
http://forums.rennlist.com/rennforums/showthread.php?t=311755&highlight=key+range
The fob might also just need a reset. Here's a link to a Renntech thread that detailed how to reset the key fob. You may need to register first.
http://www.renntech.org/forums/index.php?showtopic=7409&hl=key+fob