Went to a certain big box store today (not the one that's a person's name, the other one) and found Season 2, complete with 3D glasses (I've checked and they're in there) for 17 dollars. Best price by far I've seen it going for, and I thought the 3D versions were all gone, too!
I was able to buy a limited edition set from Best Buy. It seems they still have them in stock, but it's hard to find: http://www.bestbuy.com/site/Chuck%3A+Complete+Second+Season+With+Exclusive+Mini+Comic+-+DVD/9641393.p?id=2064458&skuId=9641393&st=Chuck:%20The%20Complete%20Second%20Season&lp=3&cp=1
Yow! The 3D ed is very hit & miss. You can occasionally find one on ebay at a decent price, but some of those sellers are asking for upwards of $100, the idiots. Costco has these on sale right now, so I checked the Madison, WI Costco. They had S1 & S3. No S2. I checked 2 SuperTargets. They both had S1 & S3. No S2. The best/biggest Barnes & Noble around had 2 copies of S2, but neither were the 3D ed. The local Best Buy had 1 copy of S2, but it was the non-3D ed. I was about to give up looking. Strolled into a small, cruddy Target. They had 1 copy of S2 3D ed left!