What merchants should use, only they should know!
I use https://walletbit.com
They already have some modules done for opensource ecommerce platforms.
With walletbit it looks like the customer NEEDS to have walletbit as well as me, the seller. Is this correct?
For me it suits me well, because i needed the module for a digital downloads shop, and using WalletBit, payments get confirmed instantly.
If they accepted payments straight from the bitcoin client that wouldn't be possible at all.