I was using only 1 naturalize, but I'm back to two again. The number of times you can force opponents to destroy cards via naturalize is amazing. Especially against handlocks. They save up for that first giant, then drop him down and have 8 or 9 cards in hand. If you can naturalize it, they go to 10, maybe 11 (destroys 11th card), and then they lose another on their draw. I recently played a priest who was holding 9 cards. I played Ysera, thinking he'd probably mind control her. Sure enough, he drew, then mind controlled Ysera (back to 9 cards). I naturalized, he lost her, then he lost a Rag that he would have drawn as well. He threw down a druid of the claw that he'd stolen earlier from me and healed up, I naturalized it as well, and he lost 2 more cards - not really important ones, but its still two cards. Miracle rogues can run into a lot of problems with this too - they get down that auctioneer and manage to draw a ton of cards, but have to restealth him because they don't have win conditions yet. Then you naturalize whatever else you can and suddenly they're losing cards or even taking fatigue.
Sometimes you can double naturalize their creatures on the same turn when they already have 8 or 9 cards in hand, and they not only lose the two creatures, they lose 2-3 cards drawn. Against any control deck, it can be very effective, and having two seems three or four times as good as 1, not just double, because often they wouldn't have cards destroyed if you couldn't double naturalize them. I love situations like these, because you also get to see the cards they lose from over drawing, and the number of times I've seen people lose a legendary or epic is amazing.
Against some weenie decks it can be very bad of course, but there are a lot of games where you can naturalize that doomguard, knowing he already discarded the other with a soulfire/his first doomguard, and there are no more big threats to get through your heavy taunters left in the deck, if you can just block some minions with that ancient of war, or survive long enough to heal up with that ancient of lore you've been trying to live long enough to cast. Most those decks can stall out if you can remove 1 or 2 big cards. Ya it sucks to give up card advantage, but sometimes that 1 mana removal can be a life saver or a game winner.