Man, I must run through this scenario in my head over and over. My e36 is a bit small to keep using as a family vehicle. I definitely have a car seat in it without too much trouble, but I have to have the passenger seat all the way forward to do it.
Staying in the BMW world and your price range, you have e46 and e39 wagons. The e39 gives you about 1.5" more rear leg room and way more rear cargo space....they're just kinda ugly. I love e39 sedans, but they jacked the proportions all up for the wagons. Which leaves an e46 wagon which looks good, but isn't the biggest. I keep coming back to the e46 wagon just because it's somewhat familiar and easy to work on for me.
Audi wise, the A4 wagons are similar in interio dimmensions as the comparable year 3 series wagons. If you get a turbo 4cyl A4 you can make it pretty peppy for not too much investment or trouble. A6 wagons are similar to 5 series. The A6 gets you about 2" more rear leg room which is nice.
Even though they're out of your price range, 2006-ish A6s are attractive. They don't have the air suspension and 2.7T of the allroad, but don't have those issues either. They're just going to be slow and boring.
http://www.autotrader.com/cars-for-sale/vehicledetails.xhtml?zip=43081&endYear=2007&modelCode1=A6&startYear=2004&makeCode1=AUDI&bodyStyles=WAGON&searchRadius=500&maxPrice=20000&listingId=326277463&Log=0