I recently fresh installed the machine with the wallet (12/8). It is a htpc, gaming, and bitcoin miner on the side.  The wallet was taken down to about .1 btc, and i've kept it around there since I noticed it.  My password is a long random string stored in an encrypted file which I copy+pasted each time.  Although a good keylogger would have picked that up as well.

My outbound transactions this year were on 5/8 (to bitconica :sad:), 9/24, 11/13, & 12/5.  So unless it was compromised much earlier than pull on 1/13, I don't know know how else it could have happend.  I guess I'll be reloading from scratch this weekend either way.  

The receiving address received a number of smallish transactions on 1/13 hours before mine and then stopped.  Other victims?

https://blockchain.info/address/1PvbGt9kkZikdNkFZDkLGtMgbD8gWMNeor

But the advice on paper wallets will be taken into account going forward.

Yes, the native client is the only thing I've ever used. 

I've been mining for a while now, but I opened my wallet and 47.1 bitcoins were transferred away from my encrypted wallet.    Was it hacked somehow?

https://blockchain.info/tx/bf6379b69acbe6e1ea95970dedf858c7908a00ada609a570fd45e558220bcd2c