I accept bitcoins at casascius.com for physical goods. It's really easy and you don't need to run any bitcoin software on your web server.
1. Pre-generate a large number of bitcoin addresses (10000+). You could do this into a CSV file at BitAddress.org.
2. Put the bitcoin addresses in a database table on your web server. (Don't put the wallet/privatekeys on your web server, otherwise you risk hackers stealing your coins. Just the addresses as they will be shown to customers.)
3. Each time you get an order, dispense one of the addresses to the customer as his "payment address" and save it with the order.
4. Whatever notifies you of a new order (an e-mail? a web page?), add a link to Block Explorer with the address dedicated to that order, so you can click it and confirm payment was made. Transactions don't show up on Block Explorer until they get confirmed into a block (usually 5-10 min but can take an hour), but if you're shipping physical goods, it doesn't much matter. The link will be http://www.blockexplorer.com/address/THEADDRESSGOESHERE
5. Bitcoins will safely pile up on the block chain. Use the original wallet file you generated in step 1 to spend them.