If you mean how do you implement shopping cards and such with bitcoins, then you're looking for the json interface to bitcoind
I would
strongly discourage this approach. It requires the online store to keep the wallet online, which is extremely hard to secure properly. It also requires setting up bitcoind daemon and custom JSON/RPC integration, which is not trivial for most Merchants. It's far better to use one of existing merchants solutions.
Well unfortunately you are a bit biased. After recent events the reliability of third parties to manage bitcoins must always be considered lower then managing your own wallets and security. The entire point of bitcoin is to eliminate the need for third parties, that's a security feature you should not attempt to circumvent unless you thoroughly understand and can tolerate the risks involved.
Also, in point of fact. You do not need to keep a wallet that contains coins in it on the server if you are only receiving payments. You can pre-generate a number of bitcoin addresses on a secure client and load them into a database table on your site. Even if you do use a normal server side bitcoind you can also keep a local copy of the same wallet, so that you can regularly sweep money to your trading account of offline savings wallet.