How can I best implement Bitcoin in my business? Is there any good tutorial, discussion or implementation of bitcoind for business?
What's the best Bitcoin.conf?
How to expose the Bitcoind API to the internet?
How to guarantee confidentiality, integrity and availability? 


Basically I'm looking for advices on how not to turn my small online shop into the new mybitcoin.com :)
Just some quick tips to get you started:


run with 'noirc=1' so that your node IP isn't discoverable via IRC
run with several 'connect=' so your node only connects to other specific nodes that you trust
do not expose the json api to the internet at large, confine it to localhost or specific ip only.
if you plan to hold a significant amount of bitcoins, then estimate how many you'll need for your daily float, and save the rest in an offline wallet (also generated on an offline computer - don't leave traces of your keys on any internet-connected disk)
do not accept 0-confirmation transactions, other than for really trivial amounts where speed of delivery is of the essence.
do use new bitcoin addresses for every new customer and order. address reuse makes it easier to track your customers.


There are probably a more items that could be added to the list, this is certainly not to be treated as comprehensive.