Here are some rust areas to look out for...if buying something sight unseen (like Ebay) you should always request pictures of these areas if you can.
AC Drain Issue
There is a little rubber elbow (at least on the 94-96 Wagons) on the passenger side firewall that allows water from the AC to drain out.
Most wagons are missing this...also, even if you still have the elbow attached, water can not drain properly.
Lift up the front passenger side footwell carpet and look for rust. Sometimes it can be so bad that you can see rust eating through from the underbelly on that side. This water can also lead to mold in the carpet and pad
You should add a length of tube to the elbow so that the water can drain properly under the car.
Some folks say the whole AC drain thing is BS. But I have seen this happen personally and added the hose to divert the drain water....and no more wet carpet.
Front body to frame mounts
These are known weak areas on the wagons (and likely sedans) Crud collects in this area and rust can weaken the body area. These mounts are located at the bottom of the firewall/top of frame and can be viewed from under the wagon.
http://i418.photobucket.com/albums/pp261/chrisandcarapowell/Project WWW/IMG_7576.jpg
http://i418.photobucket.com/albums/pp261/chrisandcarapowell/Project WWW/IMG_7581.jpg
Rear Wheelwell area
You will likely need to remove the wheel to get a good look...but one can feel around and see if any rot is present. This is the area above the frame in the rear wheelwell. Some rot can be minor, but soemtimes it can go all the way through to the inside. Look carefully...and if you see some (as in the pic below) Poke at it if you can to see how deep it goes.
http://i418.photobucket.com/albums/pp261/chrisandcarapowell/Project WWW/IMG_6814.jpg
Tailgate area and D pillar
Look for rust in the tailgate jamb and under the tailgate door. Look around the hinges carefully and pull out the taillights too. Pull up the top of the bumper cover (just push clips holding it in) and take a peek under there as well.
http://i418.photobucket.com/albums/pp261/chrisandcarapowell/Project WWW/roady11.jpg
The D pillar can be nasty...peek behind the tops of the taillights to see if any rust is bubbling. If it has...that whole area must be cut out/replaced to fix it right. Might not be the wagon for you. Look to see if that area has been repainted. If it has, ask how the repair was done. I have seen the results of the "bondo" repair. The bubbling always comes back.
http://i418.photobucket.com/albums/pp261/chrisandcarapowell/SS_FORUM/LongRoof_Forum/RobsCar047.jpg
B Pillar area
This is also another common area that can rust out. Check carefully and pull back the plastic trim as well.
http://i418.photobucket.com/albums/pp261/chrisandcarapowell/SS_FORUM/LongRoof_Forum/B-Pillar.jpg